From ffda6607a18b09d6320f597c96a0e18039702749 Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 11 Feb 2026 15:10:41 +0000 Subject: [PATCH] Build branch openpipeline/v4.0 with version v4.0.2 to openpipeline on branch v4.0 (cd7beddf) Build pipeline: openpipelines-bio.openpipeline.v4.0.2-x7gmp Source commit: https://github.com/openpipelines-bio/openpipeline/commit/cd7beddfa85b60b543399a9e2554b8e7b8eaaf62 Source message: Bump version to v4.0.2 --- CHANGELOG.md | 6 +++ _viash.yaml | 2 +- .../from_cellranger_multi_to_h5mu/script.py | 2 +- .../from_cellranger_multi_to_h5mu/test.py | 40 +++++++++++++++++++ .../filter/delimit_counts/.config.vsh.yaml | 10 ++--- .../filter/delimit_counts/delimit_counts | 14 +++---- .../.config.vsh.yaml | 10 ++--- .../move_mudata_obs_to_tiledb | 14 +++---- .../.config.vsh.yaml | 10 ++--- .../move_mudata_obsm_to_tiledb | 14 +++---- .../.config.vsh.yaml | 10 ++--- .../move_mudata_obsp_to_tiledb | 14 +++---- .../filter/delimit_counts/.config.vsh.yaml | 10 ++--- 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.../annotation/scanvi_scarches/main.nf | 10 ++--- .../scanvi_scarches/nextflow.config | 2 +- .../annotation/scvi_knn/.config.vsh.yaml | 8 ++-- .../workflows/annotation/scvi_knn/main.nf | 10 ++--- .../annotation/scvi_knn/nextflow.config | 2 +- .../pseudobulk_deseq2/.config.vsh.yaml | 8 ++-- .../pseudobulk_deseq2/main.nf | 10 ++--- .../pseudobulk_deseq2/nextflow.config | 2 +- .../gdo/gdo_singlesample/.config.vsh.yaml | 8 ++-- .../workflows/gdo/gdo_singlesample/main.nf | 10 ++--- .../gdo/gdo_singlesample/nextflow.config | 2 +- .../ingestion/bd_rhapsody/.config.vsh.yaml | 8 ++-- .../workflows/ingestion/bd_rhapsody/main.nf | 10 ++--- .../ingestion/bd_rhapsody/nextflow.config | 2 +- .../cellranger_mapping/.config.vsh.yaml | 8 ++-- .../ingestion/cellranger_mapping/main.nf | 10 ++--- .../cellranger_mapping/nextflow.config | 2 +- .../cellranger_multi/.config.vsh.yaml | 8 ++-- .../ingestion/cellranger_multi/main.nf | 10 ++--- .../cellranger_multi/nextflow.config | 2 +- .../.config.vsh.yaml | 8 ++-- .../cellranger_postprocessing/main.nf | 10 ++--- .../cellranger_postprocessing/nextflow.config | 2 +- .../ingestion/conversion/.config.vsh.yaml | 8 ++-- .../workflows/ingestion/conversion/main.nf | 10 ++--- .../ingestion/conversion/nextflow.config | 2 +- .../ingestion/demux/.config.vsh.yaml | 8 ++-- .../workflows/ingestion/demux/main.nf | 10 ++--- .../workflows/ingestion/demux/nextflow.config | 2 +- .../ingestion/make_reference/.config.vsh.yaml | 8 ++-- .../ingestion/make_reference/main.nf | 10 ++--- .../ingestion/make_reference/nextflow.config | 2 +- .../integration/bbknn_leiden/.config.vsh.yaml | 8 ++-- .../integration/bbknn_leiden/main.nf | 10 ++--- .../integration/bbknn_leiden/nextflow.config | 2 +- .../harmony_leiden/.config.vsh.yaml | 8 ++-- .../integration/harmony_leiden/main.nf | 10 ++--- .../harmony_leiden/nextflow.config | 2 +- .../scanorama_leiden/.config.vsh.yaml | 8 ++-- .../integration/scanorama_leiden/main.nf | 10 ++--- .../scanorama_leiden/nextflow.config | 2 +- .../integration/scvi_leiden/.config.vsh.yaml | 8 ++-- .../workflows/integration/scvi_leiden/main.nf | 10 ++--- .../integration/scvi_leiden/nextflow.config | 2 +- .../totalvi_leiden/.config.vsh.yaml | 8 ++-- .../integration/totalvi_leiden/main.nf | 10 ++--- .../totalvi_leiden/nextflow.config | 2 +- .../totalvi_scarches_leiden/.config.vsh.yaml | 8 ++-- .../totalvi_scarches_leiden/main.nf | 10 ++--- .../totalvi_scarches_leiden/nextflow.config | 2 +- .../dimensionality_reduction/.config.vsh.yaml | 8 ++-- .../dimensionality_reduction/main.nf | 10 ++--- .../dimensionality_reduction/nextflow.config | 2 +- .../neighbors_leiden_umap/.config.vsh.yaml | 8 ++-- .../multiomics/neighbors_leiden_umap/main.nf | 10 ++--- .../neighbors_leiden_umap/nextflow.config | 2 +- .../process_batches/.config.vsh.yaml | 8 ++-- .../multiomics/process_batches/main.nf | 10 ++--- .../process_batches/nextflow.config | 2 +- .../process_samples/.config.vsh.yaml | 8 ++-- .../multiomics/process_samples/main.nf | 10 ++--- .../process_samples/nextflow.config | 2 +- .../prot/prot_multisample/.config.vsh.yaml | 8 ++-- .../workflows/prot/prot_multisample/main.nf | 10 ++--- .../prot/prot_multisample/nextflow.config | 2 +- .../prot/prot_singlesample/.config.vsh.yaml | 8 ++-- .../workflows/prot/prot_singlesample/main.nf | 10 ++--- .../prot/prot_singlesample/nextflow.config | 2 +- .../nextflow/workflows/qc/qc/.config.vsh.yaml | 8 ++-- target/nextflow/workflows/qc/qc/main.nf | 10 ++--- .../nextflow/workflows/qc/qc/nextflow.config | 2 +- .../rna/rna_multisample/.config.vsh.yaml | 8 ++-- .../workflows/rna/rna_multisample/main.nf | 10 ++--- .../rna/rna_multisample/nextflow.config | 2 +- .../rna/rna_singlesample/.config.vsh.yaml | 8 ++-- .../workflows/rna/rna_singlesample/main.nf | 10 ++--- .../rna/rna_singlesample/nextflow.config | 2 +- 804 files changed, 3897 insertions(+), 3851 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c7d8cb36..997482d3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# openpipelines 4.0.2 + +## BUG FIXES + +* `convert/from_cellranger_multi_to_h5mu`: fix converting Cell Ranger output that contains no feature reference CSV file (PR #1136) + # openpipelines 4.0.1 ## BUG FIXES diff --git a/_viash.yaml b/_viash.yaml index dd581320..07622279 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ viash_version: 0.9.4 -version: v4.0.1 +version: v4.0.2 source: src target: target # Note: this causes the docker images to be renamed diff --git a/src/convert/from_cellranger_multi_to_h5mu/script.py b/src/convert/from_cellranger_multi_to_h5mu/script.py index d75223ba..9307f648 100644 --- a/src/convert/from_cellranger_multi_to_h5mu/script.py +++ b/src/convert/from_cellranger_multi_to_h5mu/script.py @@ -150,7 +150,7 @@ def gather_input_data(dir: Path): found_input["count"] = dir feature_reference = found_input["count"] / "feature_reference.csv" - if feature_reference: + if feature_reference.is_file(): found_input["feature_reference"] = feature_reference per_sample_outs_dir = dir / "per_sample_outs" diff --git a/src/convert/from_cellranger_multi_to_h5mu/test.py b/src/convert/from_cellranger_multi_to_h5mu/test.py index 2324bea5..688c824d 100644 --- a/src/convert/from_cellranger_multi_to_h5mu/test.py +++ b/src/convert/from_cellranger_multi_to_h5mu/test.py @@ -2,6 +2,7 @@ import sys import pytest import math from mudata import read_h5mu +from shutil import copytree ## VIASH START meta = { @@ -277,5 +278,44 @@ def test_antibody_and_cell_barcode_probes(run_component, tmp_path, input_4plex_d assert list(converted_data.mod.keys()) == ["rna", "prot"] +def test_no_feature_reference(run_component, tmp_path, input_4plex_dtc): + # Create a copy of the input without a feature reference + input_without_feature_reference = tmp_path / "input_without_feature_reference" + copytree(input_4plex_dtc, input_without_feature_reference) + try: + (input_without_feature_reference / "feature_reference.csv").unlink() + except FileNotFoundError: + ( + input_without_feature_reference + / "multi" + / "count" + / "feature_reference.csv" + ).unlink() + output_dir = tmp_path / "converted" + output_path_template = output_dir / "*.h5mu" + samples_csv = tmp_path / "samples.csv" + # run component + run_component( + [ + "--input", + input_without_feature_reference, + "--output", + str(output_path_template), + "--output_compression", + "gzip", + "--sample_csv", + samples_csv, + ] + ) + assert output_dir.is_dir() + + # check output + samples = [item for item in output_dir.iterdir() if item.is_file()] + assert len(samples) == 4 + output_path = samples[0] + converted_data = read_h5mu(output_path) + assert list(converted_data.mod.keys()) == ["rna", "prot"] + + if __name__ == "__main__": sys.exit(pytest.main([__file__])) diff --git a/target/_private/executable/filter/delimit_counts/.config.vsh.yaml b/target/_private/executable/filter/delimit_counts/.config.vsh.yaml index 51431dd8..26726d8d 100644 --- a/target/_private/executable/filter/delimit_counts/.config.vsh.yaml +++ b/target/_private/executable/filter/delimit_counts/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "delimit_counts" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -217,7 +217,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -258,11 +258,11 @@ build_info: output: "target/_private/executable/filter/delimit_counts" executable: "target/_private/executable/filter/delimit_counts/delimit_counts" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/executable/filter/delimit_counts/delimit_counts b/target/_private/executable/filter/delimit_counts/delimit_counts index c7f0e52f..e2698fe8 100755 --- a/target/_private/executable/filter/delimit_counts/delimit_counts +++ b/target/_private/executable/filter/delimit_counts/delimit_counts @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# delimit_counts v4.0.1 +# delimit_counts v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component filter delimit_counts" -LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "delimit_counts v4.0.1" + echo "delimit_counts v4.0.2" echo "" echo "Turns an .obs column containing count values into a boolean column based on" echo "thresholds." @@ -680,7 +680,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "delimit_counts v4.0.1" + echo "delimit_counts v4.0.2" exit ;; --input) @@ -864,7 +864,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_counts:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_counts:v4.0.2' fi # print dockerfile diff --git a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml index 8fdf85e5..e4966ca1 100644 --- a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml +++ b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_mudata_obs_to_tiledb" namespace: "tiledb" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -243,7 +243,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -288,11 +288,11 @@ build_info: output: "target/_private/executable/tiledb/move_mudata_obs_to_tiledb" executable: "target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -322,7 +322,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb index 9a88fecf..1bd85f16 100755 --- a/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb +++ b/target/_private/executable/tiledb/move_mudata_obs_to_tiledb/move_mudata_obs_to_tiledb @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_mudata_obs_to_tiledb v4.0.1 +# move_mudata_obs_to_tiledb v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component tiledb move_mudata_obs_to_tiledb" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_mudata_obs_to_tiledb v4.0.1" + echo "move_mudata_obs_to_tiledb v4.0.2" echo "" echo "Move .obs columns from a MuData modality to an existing tileDB database." echo "The .obs keys should not exist in the database yet; and the observations from" @@ -686,7 +686,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_mudata_obs_to_tiledb v4.0.1" + echo "move_mudata_obs_to_tiledb v4.0.2" exit ;; --input_uri) @@ -904,7 +904,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obs_to_tiledb:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obs_to_tiledb:v4.0.2' fi # print dockerfile diff --git a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml index ecee9f39..221e5cee 100644 --- a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml +++ b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_mudata_obsm_to_tiledb" namespace: "tiledb" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -220,7 +220,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -265,11 +265,11 @@ build_info: output: "target/_private/executable/tiledb/move_mudata_obsm_to_tiledb" executable: "target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -299,7 +299,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb index 53d6d9d7..0e72c268 100755 --- a/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb +++ b/target/_private/executable/tiledb/move_mudata_obsm_to_tiledb/move_mudata_obsm_to_tiledb @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_mudata_obsm_to_tiledb v4.0.1 +# move_mudata_obsm_to_tiledb v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component tiledb move_mudata_obsm_to_tiledb" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_mudata_obsm_to_tiledb v4.0.1" + echo "move_mudata_obsm_to_tiledb v4.0.2" echo "" echo "Move .obsm items from a MuData modality to an existing tileDB database." echo "The .obsm keys should not exist in the database yet; and the observations from" @@ -675,7 +675,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_mudata_obsm_to_tiledb v4.0.1" + echo "move_mudata_obsm_to_tiledb v4.0.2" exit ;; --input_uri) @@ -871,7 +871,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsm_to_tiledb:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsm_to_tiledb:v4.0.2' fi # print dockerfile diff --git a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml index 5b4b236b..6cbd3cf9 100644 --- a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml +++ b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_mudata_obsp_to_tiledb" namespace: "tiledb" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -220,7 +220,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -265,11 +265,11 @@ build_info: output: "target/_private/executable/tiledb/move_mudata_obsp_to_tiledb" executable: "target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -299,7 +299,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb index 3f3281f7..ff3dac4b 100755 --- a/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb +++ b/target/_private/executable/tiledb/move_mudata_obsp_to_tiledb/move_mudata_obsp_to_tiledb @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_mudata_obsp_to_tiledb v4.0.1 +# move_mudata_obsp_to_tiledb v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component tiledb move_mudata_obsp_to_tiledb" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_mudata_obsp_to_tiledb v4.0.1" + echo "move_mudata_obsp_to_tiledb v4.0.2" echo "" echo "Move .obsp items from a MuData modality to an existing tileDB database." echo "The .obsp keys should not exist in the database yet; and the observations from" @@ -675,7 +675,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_mudata_obsp_to_tiledb v4.0.1" + echo "move_mudata_obsp_to_tiledb v4.0.2" exit ;; --input_uri) @@ -871,7 +871,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsp_to_tiledb:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/tiledb/move_mudata_obsp_to_tiledb:v4.0.2' fi # print dockerfile diff --git a/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml b/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml index b831ed12..819c7b4d 100644 --- a/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml +++ b/target/_private/nextflow/filter/delimit_counts/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "delimit_counts" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -217,7 +217,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -258,11 +258,11 @@ build_info: output: "target/_private/nextflow/filter/delimit_counts" executable: "target/_private/nextflow/filter/delimit_counts/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/filter/delimit_counts/main.nf b/target/_private/nextflow/filter/delimit_counts/main.nf index 017d6fd1..9300a90c 100644 --- a/target/_private/nextflow/filter/delimit_counts/main.nf +++ b/target/_private/nextflow/filter/delimit_counts/main.nf @@ -1,4 +1,4 @@ -// delimit_counts v4.0.1 +// delimit_counts v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "delimit_counts", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3309,7 +3309,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3365,12 +3365,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_private/nextflow/filter/delimit_counts", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3395,7 +3395,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3940,7 +3940,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/delimit_counts", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/_private/nextflow/filter/delimit_counts/nextflow.config b/target/_private/nextflow/filter/delimit_counts/nextflow.config index cff4fa2e..e02a80a0 100644 --- a/target/_private/nextflow/filter/delimit_counts/nextflow.config +++ b/target/_private/nextflow/filter/delimit_counts/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/delimit_counts' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Turns an .obs column containing count values into a boolean column based on thresholds.\n' author = 'Dorien Roosen' } diff --git a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml index 484f5d90..06b58500 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml +++ b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_mudata_obs_to_tiledb" namespace: "tiledb" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -243,7 +243,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -288,11 +288,11 @@ build_info: output: "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb" executable: "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -322,7 +322,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf index 85daad83..2f63eb9e 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf +++ b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/main.nf @@ -1,4 +1,4 @@ -// move_mudata_obs_to_tiledb v4.0.1 +// move_mudata_obs_to_tiledb v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "move_mudata_obs_to_tiledb", "namespace" : "tiledb", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3333,7 +3333,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3393,12 +3393,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3423,7 +3423,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4012,7 +4012,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/tiledb/move_mudata_obs_to_tiledb", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config index 4a57f077..6847cf7e 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config +++ b/target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'tiledb/move_mudata_obs_to_tiledb' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Move .obs columns from a MuData modality to an existing tileDB database.\nThe .obs keys should not exist in the database yet; and the observations from the modality and \ntheir order should match with what is already present the tiledb database.\n' author = 'Dries Schaumont' } diff --git a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml index e3b3e823..a5266978 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml +++ b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_mudata_obsm_to_tiledb" namespace: "tiledb" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -220,7 +220,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -265,11 +265,11 @@ build_info: output: "target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb" executable: "target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -299,7 +299,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf index e8f53850..33987397 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf +++ b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/main.nf @@ -1,4 +1,4 @@ -// move_mudata_obsm_to_tiledb v4.0.1 +// move_mudata_obsm_to_tiledb v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "move_mudata_obsm_to_tiledb", "namespace" : "tiledb", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3307,7 +3307,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3367,12 +3367,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3397,7 +3397,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3977,7 +3977,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/tiledb/move_mudata_obsm_to_tiledb", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config index 01b1b7a4..f9aa98d3 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config +++ b/target/_private/nextflow/tiledb/move_mudata_obsm_to_tiledb/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'tiledb/move_mudata_obsm_to_tiledb' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Move .obsm items from a MuData modality to an existing tileDB database.\nThe .obsm keys should not exist in the database yet; and the observations from the modality and \ntheir order should match with what is already present the tiledb database.\n' author = 'Dries Schaumont' } diff --git a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml index dc8ce008..c6c09322 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml +++ b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_mudata_obsp_to_tiledb" namespace: "tiledb" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -220,7 +220,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -265,11 +265,11 @@ build_info: output: "target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb" executable: "target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -299,7 +299,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf index 2d6a0b7e..b189abbf 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf +++ b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/main.nf @@ -1,4 +1,4 @@ -// move_mudata_obsp_to_tiledb v4.0.1 +// move_mudata_obsp_to_tiledb v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "move_mudata_obsp_to_tiledb", "namespace" : "tiledb", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3307,7 +3307,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3367,12 +3367,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3397,7 +3397,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3965,7 +3965,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/tiledb/move_mudata_obsp_to_tiledb", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config index 9f5cdc01..1d3b2137 100644 --- a/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config +++ b/target/_private/nextflow/tiledb/move_mudata_obsp_to_tiledb/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'tiledb/move_mudata_obsp_to_tiledb' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Move .obsp items from a MuData modality to an existing tileDB database.\nThe .obsp keys should not exist in the database yet; and the observations from the modality and \ntheir order should match with what is already present the tiledb database.\n' author = 'Dries Schaumont' } diff --git a/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml b/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml index 86196302..826a0693 100644 --- a/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml +++ b/target/_private/nextflow/workflows/multiomics/split_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_h5mu" namespace: "workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -212,13 +212,13 @@ build_info: output: "target/_private/nextflow/workflows/multiomics/split_h5mu" executable: "target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/dataflow/split_h5mu" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -248,7 +248,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf b/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf index e431128f..9edc3a3a 100644 --- a/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf +++ b/target/_private/nextflow/workflows/multiomics/split_h5mu/main.nf @@ -1,4 +1,4 @@ -// split_h5mu v4.0.1 +// split_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "split_h5mu", "namespace" : "workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3305,12 +3305,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/_private/nextflow/workflows/multiomics/split_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3335,7 +3335,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config b/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config index 7b86fe22..d0997581 100644 --- a/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config +++ b/target/_private/nextflow/workflows/multiomics/split_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/split_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. ' author = 'Dries Schaumont' } diff --git a/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml b/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml index 343a3c0e..3d4b2afa 100644 --- a/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml +++ b/target/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_modalities" namespace: "workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -183,13 +183,13 @@ build_info: output: "target/_private/nextflow/workflows/multiomics/split_modalities" executable: "target/_private/nextflow/workflows/multiomics/split_modalities/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/dataflow/split_modalities" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -219,7 +219,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf b/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf index 01abda2b..e1ba4223 100644 --- a/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf +++ b/target/_private/nextflow/workflows/multiomics/split_modalities/main.nf @@ -1,4 +1,4 @@ -// split_modalities v4.0.1 +// split_modalities v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "split_modalities", "namespace" : "workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3274,12 +3274,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/_private/nextflow/workflows/multiomics/split_modalities", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3304,7 +3304,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config b/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config index 24eb55e1..14e373d7 100644 --- a/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config +++ b/target/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/split_modalities' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A pipeline to split a multimodal mudata files into several unimodal mudata files.' author = 'Dries Schaumont' } diff --git a/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml b/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml index 2c4d3598..e0c2fda2 100644 --- a/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml +++ b/target/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "log_normalize" namespace: "workflows/rna" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -198,7 +198,7 @@ build_info: output: "target/_private/nextflow/workflows/rna/log_normalize" executable: "target/_private/nextflow/workflows/rna/log_normalize/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/transform/normalize_total" @@ -206,7 +206,7 @@ build_info: - "target/nextflow/transform/delete_layer" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -236,7 +236,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_private/nextflow/workflows/rna/log_normalize/main.nf b/target/_private/nextflow/workflows/rna/log_normalize/main.nf index b2355135..d2e13de1 100644 --- a/target/_private/nextflow/workflows/rna/log_normalize/main.nf +++ b/target/_private/nextflow/workflows/rna/log_normalize/main.nf @@ -1,4 +1,4 @@ -// log_normalize v4.0.1 +// log_normalize v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "log_normalize", "namespace" : "workflows/rna", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3294,12 +3294,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/_private/nextflow/workflows/rna/log_normalize", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3324,7 +3324,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config b/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config index b8d823cb..d3ea2995 100644 --- a/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config +++ b/target/_private/nextflow/workflows/rna/log_normalize/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/rna/log_normalize' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs normalization and subsequent log-transformation of raw count data.' author = 'Dries Schaumont' } diff --git a/target/_test/executable/download/sync_test_resources/.config.vsh.yaml b/target/_test/executable/download/sync_test_resources/.config.vsh.yaml index eabb62bb..3333600e 100644 --- a/target/_test/executable/download/sync_test_resources/.config.vsh.yaml +++ b/target/_test/executable/download/sync_test_resources/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "sync_test_resources" namespace: "download" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -174,7 +174,7 @@ engines: id: "docker" image: "amazon/aws-cli:2.17.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "yum" @@ -195,11 +195,11 @@ build_info: output: "target/_test/executable/download/sync_test_resources" executable: "target/_test/executable/download/sync_test_resources/sync_test_resources" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -229,7 +229,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/download/sync_test_resources/sync_test_resources b/target/_test/executable/download/sync_test_resources/sync_test_resources index 86aa3ffa..43f97d34 100755 --- a/target/_test/executable/download/sync_test_resources/sync_test_resources +++ b/target/_test/executable/download/sync_test_resources/sync_test_resources @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# sync_test_resources v4.0.1 +# sync_test_resources v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component download sync_test_resources" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "sync_test_resources v4.0.1" + echo "sync_test_resources v4.0.2" echo "" echo "Sync test resources to the local filesystem" echo "" @@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "sync_test_resources v4.0.1" + echo "sync_test_resources v4.0.2" exit ;; --input) @@ -821,7 +821,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/sync_test_resources:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/sync_test_resources:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml index 9ed8015f..b5ef91f5 100644 --- a/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/annotation/celltypist_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "celltypist_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -131,7 +131,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -164,11 +164,11 @@ build_info: output: "target/_test/executable/test_workflows/annotation/celltypist_test" executable: "target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -198,7 +198,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test b/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test index db25f6c0..a671bcd0 100755 --- a/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test +++ b/target/_test/executable/test_workflows/annotation/celltypist_test/celltypist_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# celltypist_test v4.0.1 +# celltypist_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation celltypist_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "celltypist_test v4.0.1" + echo "celltypist_test v4.0.2" echo "" echo "This component tests the output of the annotation of the celltypist workflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "celltypist_test v4.0.1" + echo "celltypist_test v4.0.2" exit ;; --input) @@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/celltypist_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/celltypist_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml index 7c7ac57d..bba7c5ec 100644 --- a/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "harmony_knn_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/annotation/harmony_knn_test" executable: "target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test b/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test index 34af522b..7dcab7b0 100755 --- a/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test +++ b/target/_test/executable/test_workflows/annotation/harmony_knn_test/harmony_knn_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# harmony_knn_test v4.0.1 +# harmony_knn_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation harmony_knn_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "harmony_knn_test v4.0.1" + echo "harmony_knn_test v4.0.2" echo "" echo "This component tests the output of the annotation of the harmony_knn of" echo "workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "harmony_knn_test v4.0.1" + echo "harmony_knn_test v4.0.2" exit ;; --input) @@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/harmony_knn_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/harmony_knn_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml index 6b1fc245..1479ef33 100644 --- a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanvi_scarches_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/annotation/scanvi_scarches_test" executable: "target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test index 6ae3a63c..3951a2fc 100755 --- a/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test +++ b/target/_test/executable/test_workflows/annotation/scanvi_scarches_test/scanvi_scarches_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scanvi_scarches_test v4.0.1 +# scanvi_scarches_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation scanvi_scarches_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scanvi_scarches_test v4.0.1" + echo "scanvi_scarches_test v4.0.2" echo "" echo "This component tests the output of the annotation of the scanvi annotation" echo "workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scanvi_scarches_test v4.0.1" + echo "scanvi_scarches_test v4.0.2" exit ;; --input) @@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scanvi_scarches_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scanvi_scarches_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml index e6cc3209..a4c35ac2 100644 --- a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scgpt_annotation_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -129,7 +129,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -162,11 +162,11 @@ build_info: output: "target/_test/executable/test_workflows/annotation/scgpt_annotation_test" executable: "target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -196,7 +196,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test index e0ce72c6..9d2a4d3f 100755 --- a/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test +++ b/target/_test/executable/test_workflows/annotation/scgpt_annotation_test/scgpt_annotation_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scgpt_annotation_test v4.0.1 +# scgpt_annotation_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation scgpt_annotation_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scgpt_annotation_test v4.0.1" + echo "scgpt_annotation_test v4.0.2" echo "" echo "This component test the output of the the scgpt_annotation workflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scgpt_annotation_test v4.0.1" + echo "scgpt_annotation_test v4.0.2" exit ;; --input) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scgpt_annotation_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scgpt_annotation_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml b/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml index 056e827c..9a735f48 100644 --- a/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvi_knn_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/annotation/scvi_knn_test" executable: "target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test b/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test index 6dfecd9a..9eee3e61 100755 --- a/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test +++ b/target/_test/executable/test_workflows/annotation/scvi_knn_test/scvi_knn_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scvi_knn_test v4.0.1 +# scvi_knn_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/annotation scvi_knn_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scvi_knn_test v4.0.1" + echo "scvi_knn_test v4.0.2" echo "" echo "This component tests the output of the annotation of the scvi_knn of workflow." echo "" @@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scvi_knn_test v4.0.1" + echo "scvi_knn_test v4.0.2" exit ;; --input) @@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scvi_knn_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/annotation/scvi_knn_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml index 3a60d214..10a16023 100644 --- a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pseudobulk_deseq2_test" namespace: "test_workflows/differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -118,7 +118,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -151,11 +151,11 @@ build_info: output: "target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test" executable: "target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -185,7 +185,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test index b5eb8144..b7eb4745 100755 --- a/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test +++ b/target/_test/executable/test_workflows/differential_expression/pseudobulk_deseq2_test/pseudobulk_deseq2_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# pseudobulk_deseq2_test v4.0.1 +# pseudobulk_deseq2_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/differential_expression pseudobulk_deseq2_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:18Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "pseudobulk_deseq2_test v4.0.1" + echo "pseudobulk_deseq2_test v4.0.2" echo "" echo "This component tests the output of the pseudobulk_deseq2 differential expression" echo "analysis workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pseudobulk_deseq2_test v4.0.1" + echo "pseudobulk_deseq2_test v4.0.2" exit ;; --input) @@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/differential_expression/pseudobulk_deseq2_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/differential_expression/pseudobulk_deseq2_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml index 5b1e4d29..099f80e1 100644 --- a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/ingestion/bd_rhapsody_test" executable: "target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test index 52598709..e03eb62b 100755 --- a/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test +++ b/target/_test/executable/test_workflows/ingestion/bd_rhapsody_test/bd_rhapsody_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bd_rhapsody_test v4.0.1 +# bd_rhapsody_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion bd_rhapsody_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bd_rhapsody_test v4.0.1" + echo "bd_rhapsody_test v4.0.2" echo "" echo "This component test the output of the integration test of the bd_rhapsody" echo "workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bd_rhapsody_test v4.0.1" + echo "bd_rhapsody_test v4.0.2" exit ;; --input) @@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/bd_rhapsody_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/bd_rhapsody_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml index d62b4134..84aa0a14 100644 --- a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mapping_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/ingestion/cellranger_mapping_test" executable: "target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test index d0aebe33..384d7321 100755 --- a/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test +++ b/target/_test/executable/test_workflows/ingestion/cellranger_mapping_test/cellranger_mapping_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_mapping_test v4.0.1 +# cellranger_mapping_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion cellranger_mapping_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_mapping_test v4.0.1" + echo "cellranger_mapping_test v4.0.2" echo "" echo "This component test the output of the integration test of the cellranger mapping" echo "workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_mapping_test v4.0.1" + echo "cellranger_mapping_test v4.0.2" exit ;; --input) @@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_mapping_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_mapping_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml index 7cef69c0..6724ffd1 100644 --- a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_multi_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/ingestion/cellranger_multi_test" executable: "target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test index fc9c0af5..56ae0866 100755 --- a/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test +++ b/target/_test/executable/test_workflows/ingestion/cellranger_multi_test/cellranger_multi_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_multi_test v4.0.1 +# cellranger_multi_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion cellranger_multi_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_multi_test v4.0.1" + echo "cellranger_multi_test v4.0.2" echo "" echo "This component test the output of the integration test of the cellranger multi" echo "workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_multi_test v4.0.1" + echo "cellranger_multi_test v4.0.2" exit ;; --input) @@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_multi_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_multi_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml index a11859fb..72e6ba24 100644 --- a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_postprocessing_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -140,7 +140,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -173,11 +173,11 @@ build_info: output: "target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test" executable: "target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -207,7 +207,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test index 6958c538..c359cb3f 100755 --- a/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test +++ b/target/_test/executable/test_workflows/ingestion/cellranger_postprocessing_test/cellranger_postprocessing_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_postprocessing_test v4.0.1 +# cellranger_postprocessing_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion cellranger_postprocessing_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_postprocessing_test v4.0.1" + echo "cellranger_postprocessing_test v4.0.2" echo "" echo "This component test the output of the integration test of the cellranger" echo "postprocessing workflow." @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_postprocessing_test v4.0.1" + echo "cellranger_postprocessing_test v4.0.2" exit ;; --input) @@ -770,7 +770,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_postprocessing_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/cellranger_postprocessing_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml index ed25fab2..f8010623 100644 --- a/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/ingestion/conversion_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "conversion_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/executable/test_workflows/ingestion/conversion_test" executable: "target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test b/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test index 8c4d0e93..dfd75a39 100755 --- a/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test +++ b/target/_test/executable/test_workflows/ingestion/conversion_test/conversion_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# conversion_test v4.0.1 +# conversion_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion conversion_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "conversion_test v4.0.1" + echo "conversion_test v4.0.2" echo "" echo "This component test the output of the integration test of the conversion" echo "workflow." @@ -637,7 +637,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "conversion_test v4.0.1" + echo "conversion_test v4.0.2" exit ;; --input) @@ -739,7 +739,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/conversion_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/ingestion/conversion_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml index 12e73c80..10736993 100644 --- a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi_leiden_test" namespace: "test_workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -130,7 +130,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -163,11 +163,11 @@ build_info: output: "target/_test/executable/test_workflows/integration/totalvi_leiden_test" executable: "target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -197,7 +197,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test index 129584d0..44dc59cb 100755 --- a/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test +++ b/target/_test/executable/test_workflows/integration/totalvi_leiden_test/totalvi_leiden_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# totalvi_leiden_test v4.0.1 +# totalvi_leiden_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/integration totalvi_leiden_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:29Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:23Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "totalvi_leiden_test v4.0.1" + echo "totalvi_leiden_test v4.0.2" echo "" echo "This component tests the output of totalvi_leiden integration workflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "totalvi_leiden_test v4.0.1" + echo "totalvi_leiden_test v4.0.2" exit ;; --input) @@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/integration/totalvi_leiden_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/integration/totalvi_leiden_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml index 4b02e6fe..fcd2f84f 100644 --- a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "dimensionality_reduction_test" namespace: "test_workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -121,7 +121,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -150,11 +150,11 @@ build_info: output: "target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test" executable: "target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -184,7 +184,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test index 11042219..38acf9ac 100755 --- a/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test +++ b/target/_test/executable/test_workflows/multiomics/dimensionality_reduction_test/dimensionality_reduction_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# dimensionality_reduction_test v4.0.1 +# dimensionality_reduction_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics dimensionality_reduction_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "dimensionality_reduction_test v4.0.1" + echo "dimensionality_reduction_test v4.0.2" echo "" echo "This component test the output of the integration test of" echo "dimensionality_reduction." @@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "dimensionality_reduction_test v4.0.1" + echo "dimensionality_reduction_test v4.0.2" exit ;; --input) @@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/dimensionality_reduction_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/dimensionality_reduction_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml index 8a54f490..1bf302d7 100644 --- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "workflow_test" namespace: "test_workflows/multiomics/process_batches" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -136,7 +136,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -169,11 +169,11 @@ build_info: output: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test" executable: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -203,7 +203,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test index 2e95a9c7..7fdf8ab0 100755 --- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test +++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test/workflow_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# workflow_test v4.0.1 +# workflow_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics/process_batches workflow_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:18Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "workflow_test v4.0.1" + echo "workflow_test v4.0.2" echo "" echo "This component tests the output of the integration test of process_batches" echo "test_wf." @@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "workflow_test v4.0.1" + echo "workflow_test v4.0.2" exit ;; --input) @@ -755,7 +755,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml index 60fa90c6..8a2a523e 100644 --- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "workflow_test2" namespace: "test_workflows/multiomics/process_batches" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -136,7 +136,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -169,11 +169,11 @@ build_info: output: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2" executable: "target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -203,7 +203,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2 b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2 index 6c3ff0ac..0d86e7dc 100755 --- a/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2 +++ b/target/_test/executable/test_workflows/multiomics/process_batches/workflow_test2/workflow_test2 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# workflow_test2 v4.0.1 +# workflow_test2 v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics/process_batches workflow_test2" -LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "workflow_test2 v4.0.1" + echo "workflow_test2 v4.0.2" echo "" echo "This component tests the output of the integration test of process_batches" echo "test_wf2." @@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "workflow_test2 v4.0.1" + echo "workflow_test2 v4.0.2" exit ;; --input) @@ -755,7 +755,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test2:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test2:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml index 45d28828..660b28cf 100644 --- a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_h5mu_test" namespace: "test_workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -145,7 +145,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -178,11 +178,11 @@ build_info: output: "target/_test/executable/test_workflows/multiomics/split_h5mu_test" executable: "target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -212,7 +212,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test index c0c934df..ac4a2cbd 100755 --- a/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test +++ b/target/_test/executable/test_workflows/multiomics/split_h5mu_test/split_h5mu_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# split_h5mu_test v4.0.1 +# split_h5mu_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics split_h5mu_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "split_h5mu_test v4.0.1" + echo "split_h5mu_test v4.0.2" echo "" echo "This component test the output of the integration test of split_h5mu." echo "" @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "split_h5mu_test v4.0.1" + echo "split_h5mu_test v4.0.2" exit ;; --input) @@ -770,7 +770,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_h5mu_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_h5mu_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml b/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml index 7500dd8b..e54be734 100644 --- a/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_modalities_test" namespace: "test_workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -145,7 +145,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -178,11 +178,11 @@ build_info: output: "target/_test/executable/test_workflows/multiomics/split_modalities_test" executable: "target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -212,7 +212,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test b/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test index 02d7d64b..c5235231 100755 --- a/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test +++ b/target/_test/executable/test_workflows/multiomics/split_modalities_test/split_modalities_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# split_modalities_test v4.0.1 +# split_modalities_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics split_modalities_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "split_modalities_test v4.0.1" + echo "split_modalities_test v4.0.2" echo "" echo "This component test the output of the integration test of split_modalities." echo "" @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "split_modalities_test v4.0.1" + echo "split_modalities_test v4.0.2" exit ;; --input) @@ -770,7 +770,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_modalities_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/split_modalities_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml b/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml index 5c040cd2..9bb39150 100644 --- a/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/qc/qc_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qc_test" namespace: "test_workflows/qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -134,7 +134,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -167,11 +167,11 @@ build_info: output: "target/_test/executable/test_workflows/qc/qc_test" executable: "target/_test/executable/test_workflows/qc/qc_test/qc_test" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -201,7 +201,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/executable/test_workflows/qc/qc_test/qc_test b/target/_test/executable/test_workflows/qc/qc_test/qc_test index a71b5fab..e87b1b0e 100755 --- a/target/_test/executable/test_workflows/qc/qc_test/qc_test +++ b/target/_test/executable/test_workflows/qc/qc_test/qc_test @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# qc_test v4.0.1 +# qc_test v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/qc qc_test" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "qc_test v4.0.1" + echo "qc_test v4.0.2" echo "" echo "This component test the output of the integration test of the QC workflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "qc_test v4.0.1" + echo "qc_test v4.0.2" exit ;; --input) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/qc/qc_test:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/qc/qc_test:v4.0.2' fi # print dockerfile diff --git a/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml b/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml index 35da87a4..c53f60cb 100644 --- a/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml +++ b/target/_test/nextflow/download/sync_test_resources/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "sync_test_resources" namespace: "download" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -174,7 +174,7 @@ engines: id: "docker" image: "amazon/aws-cli:2.17.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "yum" @@ -195,11 +195,11 @@ build_info: output: "target/_test/nextflow/download/sync_test_resources" executable: "target/_test/nextflow/download/sync_test_resources/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -229,7 +229,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/download/sync_test_resources/main.nf b/target/_test/nextflow/download/sync_test_resources/main.nf index 7cd074f3..9e96ff07 100644 --- a/target/_test/nextflow/download/sync_test_resources/main.nf +++ b/target/_test/nextflow/download/sync_test_resources/main.nf @@ -1,4 +1,4 @@ -// sync_test_resources v4.0.1 +// sync_test_resources v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "sync_test_resources", "namespace" : "download", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3257,7 +3257,7 @@ meta = [ "id" : "docker", "image" : "amazon/aws-cli:2.17.11", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3285,12 +3285,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/download/sync_test_resources", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3315,7 +3315,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3801,7 +3801,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/download/sync_test_resources", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/download/sync_test_resources/nextflow.config b/target/_test/nextflow/download/sync_test_resources/nextflow.config index 388ec6af..8ce9859a 100644 --- a/target/_test/nextflow/download/sync_test_resources/nextflow.config +++ b/target/_test/nextflow/download/sync_test_resources/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'download/sync_test_resources' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Sync test resources to the local filesystem' author = 'Robrecht Cannoodt' } diff --git a/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml index 0024264c..efdf7bfd 100644 --- a/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/annotation/celltypist_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "celltypist_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -131,7 +131,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -164,11 +164,11 @@ build_info: output: "target/_test/nextflow/test_workflows/annotation/celltypist_test" executable: "target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -198,7 +198,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf b/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf index f37bf457..31f61620 100644 --- a/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf +++ b/target/_test/nextflow/test_workflows/annotation/celltypist_test/main.nf @@ -1,4 +1,4 @@ -// celltypist_test v4.0.1 +// celltypist_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "celltypist_test", "namespace" : "test_workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3200,7 +3200,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3241,12 +3241,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/celltypist_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3271,7 +3271,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3746,7 +3746,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/annotation/celltypist_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config index fc2a1851..77dc7756 100644 --- a/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/annotation/celltypist_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/annotation/celltypist_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the annotation of the celltypist workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml index 4429df59..84b81ddd 100644 --- a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "harmony_knn_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/annotation/harmony_knn_test" executable: "target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf index 8b81d949..09beb495 100644 --- a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf +++ b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/main.nf @@ -1,4 +1,4 @@ -// harmony_knn_test v4.0.1 +// harmony_knn_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "harmony_knn_test", "namespace" : "test_workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/harmony_knn_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3741,7 +3741,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/annotation/harmony_knn_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config index 85f1ba9d..cf611ee7 100644 --- a/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/annotation/harmony_knn_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/annotation/harmony_knn_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the annotation of the harmony_knn of workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml index 3bc4f91c..9f8f2a00 100644 --- a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanvi_scarches_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test" executable: "target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf index cf07c809..76abd490 100644 --- a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf +++ b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/main.nf @@ -1,4 +1,4 @@ -// scanvi_scarches_test v4.0.1 +// scanvi_scarches_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scanvi_scarches_test", "namespace" : "test_workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3737,7 +3737,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/annotation/scanvi_scarches_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config index dc37f12e..939f69b5 100644 --- a/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/annotation/scanvi_scarches_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/annotation/scanvi_scarches_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the annotation of the scanvi annotation workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml index a54e5df9..8f9d9ca2 100644 --- a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scgpt_annotation_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -129,7 +129,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -162,11 +162,11 @@ build_info: output: "target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test" executable: "target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -196,7 +196,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf index 79746256..9652983a 100644 --- a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf +++ b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/main.nf @@ -1,4 +1,4 @@ -// scgpt_annotation_test v4.0.1 +// scgpt_annotation_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scgpt_annotation_test", "namespace" : "test_workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3199,7 +3199,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3240,12 +3240,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3270,7 +3270,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3751,7 +3751,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/annotation/scgpt_annotation_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config index 59ba13c5..a327a815 100644 --- a/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/annotation/scgpt_annotation_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/annotation/scgpt_annotation_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the the scgpt_annotation workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml index 8c526b62..e7b13bee 100644 --- a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvi_knn_test" namespace: "test_workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/annotation/scvi_knn_test" executable: "target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf index 88aa8b60..6cc84f13 100644 --- a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf +++ b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/main.nf @@ -1,4 +1,4 @@ -// scvi_knn_test v4.0.1 +// scvi_knn_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scvi_knn_test", "namespace" : "test_workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/annotation/scvi_knn_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3738,7 +3738,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/annotation/scvi_knn_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config index 8463b75d..94e1ba2b 100644 --- a/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/annotation/scvi_knn_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/annotation/scvi_knn_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the annotation of the scvi_knn of workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml index a5af9560..d40dd090 100644 --- a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pseudobulk_deseq2_test" namespace: "test_workflows/differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -118,7 +118,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -151,11 +151,11 @@ build_info: output: "target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test" executable: "target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -185,7 +185,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf index 8bdb74bf..2d9e0bd6 100644 --- a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf +++ b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/main.nf @@ -1,4 +1,4 @@ -// pseudobulk_deseq2_test v4.0.1 +// pseudobulk_deseq2_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "pseudobulk_deseq2_test", "namespace" : "test_workflows/differential_expression", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3183,7 +3183,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3224,12 +3224,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3254,7 +3254,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3750,7 +3750,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/differential_expression/pseudobulk_deseq2_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config index e4b3208b..1b64d5a5 100644 --- a/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/differential_expression/pseudobulk_deseq2_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/differential_expression/pseudobulk_deseq2_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the pseudobulk_deseq2 differential expression analysis workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml index 4be11b7c..1a0d55d9 100644 --- a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test" executable: "target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf index e4a5a51b..30b4a5f7 100644 --- a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf +++ b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/main.nf @@ -1,4 +1,4 @@ -// bd_rhapsody_test v4.0.1 +// bd_rhapsody_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bd_rhapsody_test", "namespace" : "test_workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3743,7 +3743,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/ingestion/bd_rhapsody_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config index 99b72c38..23a80b80 100644 --- a/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/ingestion/bd_rhapsody_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/ingestion/bd_rhapsody_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of the bd_rhapsody workflow.' author = 'Jakub Majercik' } diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml index 3faf2103..e281e0c1 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mapping_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test" executable: "target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf index 0ef8a88c..c0dc95e2 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/main.nf @@ -1,4 +1,4 @@ -// cellranger_mapping_test v4.0.1 +// cellranger_mapping_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_mapping_test", "namespace" : "test_workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3721,7 +3721,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/ingestion/cellranger_mapping_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config index 3c66a1e8..c9bbb960 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_mapping_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/ingestion/cellranger_mapping_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of the cellranger mapping workflow.' author = 'Jakub Majercik' } diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml index c0874ca3..7c69bd35 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_multi_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test" executable: "target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf index a3c790e2..de79ee56 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/main.nf @@ -1,4 +1,4 @@ -// cellranger_multi_test v4.0.1 +// cellranger_multi_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_multi_test", "namespace" : "test_workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3725,7 +3725,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/ingestion/cellranger_multi_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config index 9c1154a0..5f3ffc85 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_multi_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/ingestion/cellranger_multi_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of the cellranger multi workflow.' author = 'Jakub Majercik' } diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml index 49c37683..89e8e96a 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_postprocessing_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -140,7 +140,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -173,11 +173,11 @@ build_info: output: "target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test" executable: "target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -207,7 +207,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf index aa9be608..c49475c3 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/main.nf @@ -1,4 +1,4 @@ -// cellranger_postprocessing_test v4.0.1 +// cellranger_postprocessing_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_postprocessing_test", "namespace" : "test_workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3210,7 +3210,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3251,12 +3251,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3281,7 +3281,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3756,7 +3756,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/ingestion/cellranger_postprocessing_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config index 9cc7771f..40ae6df2 100644 --- a/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/ingestion/cellranger_postprocessing_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/ingestion/cellranger_postprocessing_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of the cellranger postprocessing workflow.' author = 'Jakub Majercik' } diff --git a/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml index aba1044e..338e58d4 100644 --- a/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/ingestion/conversion_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "conversion_test" namespace: "test_workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -120,7 +120,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -153,11 +153,11 @@ build_info: output: "target/_test/nextflow/test_workflows/ingestion/conversion_test" executable: "target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -187,7 +187,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf index 32555d11..39002e3d 100644 --- a/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf +++ b/target/_test/nextflow/test_workflows/ingestion/conversion_test/main.nf @@ -1,4 +1,4 @@ -// conversion_test v4.0.1 +// conversion_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "conversion_test", "namespace" : "test_workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3187,7 +3187,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3228,12 +3228,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/conversion_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3258,7 +3258,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3715,7 +3715,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/ingestion/conversion_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config b/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config index 2a32461d..1e688c97 100644 --- a/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/ingestion/conversion_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/ingestion/conversion_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of the conversion workflow.' author = 'Jakub Majercik' } diff --git a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml index fcfbeda6..88d9bf01 100644 --- a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi_leiden_test" namespace: "test_workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" info: @@ -130,7 +130,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -163,11 +163,11 @@ build_info: output: "target/_test/nextflow/test_workflows/integration/totalvi_leiden_test" executable: "target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -197,7 +197,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf index ee1de4be..d1a51885 100644 --- a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf +++ b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/main.nf @@ -1,4 +1,4 @@ -// totalvi_leiden_test v4.0.1 +// totalvi_leiden_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "totalvi_leiden_test", "namespace" : "test_workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3200,7 +3200,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3241,12 +3241,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3271,7 +3271,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3751,7 +3751,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/integration/totalvi_leiden_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config index a1371e21..48cfe76f 100644 --- a/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/integration/totalvi_leiden_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/integration/totalvi_leiden_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of totalvi_leiden integration workflow.' author = 'Dorien Roosen' } diff --git a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml index be54b8cc..91ec02d7 100644 --- a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "dimensionality_reduction_test" namespace: "test_workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -121,7 +121,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -150,11 +150,11 @@ build_info: output: "target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test" executable: "target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -184,7 +184,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf index b5bb977e..d41a4cc8 100644 --- a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf +++ b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/main.nf @@ -1,4 +1,4 @@ -// dimensionality_reduction_test v4.0.1 +// dimensionality_reduction_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "dimensionality_reduction_test", "namespace" : "test_workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Kai Waldrant", @@ -3189,7 +3189,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3225,12 +3225,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3255,7 +3255,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3710,7 +3710,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/multiomics/dimensionality_reduction_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config index 615f9736..162aa898 100644 --- a/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/multiomics/dimensionality_reduction_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/multiomics/dimensionality_reduction_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of dimensionality_reduction.' author = 'Kai Waldrant' } diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml index fa634a56..47eb5f34 100644 --- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "workflow_test" namespace: "test_workflows/multiomics/process_batches" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -136,7 +136,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -169,11 +169,11 @@ build_info: output: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test" executable: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -203,7 +203,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf index 8e657edd..4b440d75 100644 --- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf +++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/main.nf @@ -1,4 +1,4 @@ -// workflow_test v4.0.1 +// workflow_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "workflow_test", "namespace" : "test_workflows/multiomics/process_batches", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Kai Waldrant", @@ -3206,7 +3206,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3247,12 +3247,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3277,7 +3277,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3744,7 +3744,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem" diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config index 99784c43..6fa176d3 100644 --- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/multiomics/process_batches/workflow_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the integration test of process_batches test_wf.' author = 'Kai Waldrant' } diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml index 655e817e..30072510 100644 --- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "workflow_test2" namespace: "test_workflows/multiomics/process_batches" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -136,7 +136,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -169,11 +169,11 @@ build_info: output: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2" executable: "target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -203,7 +203,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf index c4596863..a226b309 100644 --- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf +++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/main.nf @@ -1,4 +1,4 @@ -// workflow_test2 v4.0.1 +// workflow_test2 v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "workflow_test2", "namespace" : "test_workflows/multiomics/process_batches", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Kai Waldrant", @@ -3206,7 +3206,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3247,12 +3247,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3277,7 +3277,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3769,7 +3769,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/multiomics/process_batches/workflow_test2", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem" diff --git a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config index afd395ce..34737de2 100644 --- a/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config +++ b/target/_test/nextflow/test_workflows/multiomics/process_batches/workflow_test2/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/multiomics/process_batches/workflow_test2' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the integration test of process_batches test_wf2.' author = 'Kai Waldrant' } diff --git a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml index a627ae72..9368e9d2 100644 --- a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_h5mu_test" namespace: "test_workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -145,7 +145,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -178,11 +178,11 @@ build_info: output: "target/_test/nextflow/test_workflows/multiomics/split_h5mu_test" executable: "target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -212,7 +212,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf index 0c1e436f..8e10bd35 100644 --- a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf +++ b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/main.nf @@ -1,4 +1,4 @@ -// split_h5mu_test v4.0.1 +// split_h5mu_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "split_h5mu_test", "namespace" : "test_workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Kai Waldrant", @@ -3217,7 +3217,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3258,12 +3258,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3288,7 +3288,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3776,7 +3776,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/multiomics/split_h5mu_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config index 57f7045a..957fc97f 100644 --- a/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/multiomics/split_h5mu_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/multiomics/split_h5mu_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of split_h5mu.' author = 'Kai Waldrant' } diff --git a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml index 55f7b46b..ed23a534 100644 --- a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_modalities_test" namespace: "test_workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Kai Waldrant" info: @@ -145,7 +145,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -178,11 +178,11 @@ build_info: output: "target/_test/nextflow/test_workflows/multiomics/split_modalities_test" executable: "target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -212,7 +212,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf index 561c34b6..5ca0a0b1 100644 --- a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf +++ b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/main.nf @@ -1,4 +1,4 @@ -// split_modalities_test v4.0.1 +// split_modalities_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "split_modalities_test", "namespace" : "test_workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Kai Waldrant", @@ -3217,7 +3217,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3258,12 +3258,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/multiomics/split_modalities_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3288,7 +3288,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3778,7 +3778,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/multiomics/split_modalities_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config index ee63cc75..0f1b57f9 100644 --- a/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/multiomics/split_modalities_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/multiomics/split_modalities_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of split_modalities.' author = 'Kai Waldrant' } diff --git a/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml index ab5e78c2..600ee4d3 100644 --- a/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/qc/qc_test/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qc_test" namespace: "test_workflows/qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" info: @@ -134,7 +134,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -167,11 +167,11 @@ build_info: output: "target/_test/nextflow/test_workflows/qc/qc_test" executable: "target/_test/nextflow/test_workflows/qc/qc_test/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -201,7 +201,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/_test/nextflow/test_workflows/qc/qc_test/main.nf b/target/_test/nextflow/test_workflows/qc/qc_test/main.nf index 4158b5a8..fd780abf 100644 --- a/target/_test/nextflow/test_workflows/qc/qc_test/main.nf +++ b/target/_test/nextflow/test_workflows/qc/qc_test/main.nf @@ -1,4 +1,4 @@ -// qc_test v4.0.1 +// qc_test v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "qc_test", "namespace" : "test_workflows/qc", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3205,7 +3205,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3246,12 +3246,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/qc/qc_test", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3276,7 +3276,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3785,7 +3785,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/qc/qc_test", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config b/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config index 171f7a58..16d70fd7 100644 --- a/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config +++ b/target/_test/nextflow/test_workflows/qc/qc_test/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/qc/qc_test' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component test the output of the integration test of the QC workflow.' author = 'Jakub Majercik' } diff --git a/target/executable/annotate/celltypist/.config.vsh.yaml b/target/executable/annotate/celltypist/.config.vsh.yaml index c741a7aa..5916087e 100644 --- a/target/executable/annotate/celltypist/.config.vsh.yaml +++ b/target/executable/annotate/celltypist/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "celltypist" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -384,7 +384,7 @@ engines: id: "docker" image: "nvcr.io/nvidia/pytorch:25.11-py3" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -431,11 +431,11 @@ build_info: output: "target/executable/annotate/celltypist" executable: "target/executable/annotate/celltypist/celltypist" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -465,7 +465,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/celltypist/celltypist b/target/executable/annotate/celltypist/celltypist index 53549cd4..0a943fae 100755 --- a/target/executable/annotate/celltypist/celltypist +++ b/target/executable/annotate/celltypist/celltypist @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# celltypist v4.0.1 +# celltypist v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component annotate celltypist" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "celltypist v4.0.1" + echo "celltypist v4.0.2" echo "" echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of" echo "logistic regression classifiers optimised by the stochastic gradient descent" @@ -769,7 +769,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "celltypist v4.0.1" + echo "celltypist v4.0.2" exit ;; --input) @@ -1102,7 +1102,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/celltypist:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/celltypist:v4.0.2' fi # print dockerfile diff --git a/target/executable/annotate/onclass/.config.vsh.yaml b/target/executable/annotate/onclass/.config.vsh.yaml index 0744b49f..7202261d 100644 --- a/target/executable/annotate/onclass/.config.vsh.yaml +++ b/target/executable/annotate/onclass/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "onclass" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -365,7 +365,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -405,11 +405,11 @@ build_info: output: "target/executable/annotate/onclass" executable: "target/executable/annotate/onclass/onclass" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -439,7 +439,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/onclass/onclass b/target/executable/annotate/onclass/onclass index 839574ba..9e7334f3 100755 --- a/target/executable/annotate/onclass/onclass +++ b/target/executable/annotate/onclass/onclass @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# onclass v4.0.1 +# onclass v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component annotate onclass" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "onclass v4.0.1" + echo "onclass v4.0.2" echo "" echo "OnClass is a python package for single-cell cell type annotation. It uses the" echo "Cell Ontology to capture the cell type similarity." @@ -758,7 +758,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "onclass v4.0.1" + echo "onclass v4.0.2" exit ;; --input) @@ -1086,7 +1086,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/onclass:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/onclass:v4.0.2' fi # print dockerfile diff --git a/target/executable/annotate/popv/.config.vsh.yaml b/target/executable/annotate/popv/.config.vsh.yaml index 24475ac2..a464ee13 100644 --- a/target/executable/annotate/popv/.config.vsh.yaml +++ b/target/executable/annotate/popv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "popv" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Matthias Beyens" roles: @@ -310,7 +310,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -361,11 +361,11 @@ build_info: output: "target/executable/annotate/popv" executable: "target/executable/annotate/popv/popv" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -395,7 +395,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/popv/popv b/target/executable/annotate/popv/popv index 0f83c478..af89d6d5 100755 --- a/target/executable/annotate/popv/popv +++ b/target/executable/annotate/popv/popv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# popv v4.0.1 +# popv v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -466,10 +466,10 @@ RUN cd /opt && git clone --depth 1 https://github.com/YosefLab/PopV.git LABEL org.opencontainers.image.authors="Matthias Beyens, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component annotate popv" -LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:18Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -586,7 +586,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "popv v4.0.1" + echo "popv v4.0.2" echo "" echo "Performs popular major vote cell typing on single cell sequence data using" echo "multiple algorithms. Note that this is a one-shot version of PopV." @@ -728,7 +728,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "popv v4.0.1" + echo "popv v4.0.2" exit ;; --input) @@ -985,7 +985,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/popv:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/popv:v4.0.2' fi # print dockerfile diff --git a/target/executable/annotate/random_forest_annotation/.config.vsh.yaml b/target/executable/annotate/random_forest_annotation/.config.vsh.yaml index 0edc3ce7..72490a8c 100644 --- a/target/executable/annotate/random_forest_annotation/.config.vsh.yaml +++ b/target/executable/annotate/random_forest_annotation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "random_forest_annotation" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -373,7 +373,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -420,11 +420,11 @@ build_info: output: "target/executable/annotate/random_forest_annotation" executable: "target/executable/annotate/random_forest_annotation/random_forest_annotation" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -454,7 +454,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/random_forest_annotation/random_forest_annotation b/target/executable/annotate/random_forest_annotation/random_forest_annotation index f972ae38..fb92a16b 100755 --- a/target/executable/annotate/random_forest_annotation/random_forest_annotation +++ b/target/executable/annotate/random_forest_annotation/random_forest_annotation @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# random_forest_annotation v4.0.1 +# random_forest_annotation v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component annotate random_forest_annotation" -LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:18Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "random_forest_annotation v4.0.1" + echo "random_forest_annotation v4.0.2" echo "" echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of" echo "random forest." @@ -770,7 +770,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "random_forest_annotation v4.0.1" + echo "random_forest_annotation v4.0.2" exit ;; --input) @@ -1092,7 +1092,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/random_forest_annotation:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/random_forest_annotation:v4.0.2' fi # print dockerfile diff --git a/target/executable/annotate/scanvi/.config.vsh.yaml b/target/executable/annotate/scanvi/.config.vsh.yaml index b878af9a..a474bcf8 100644 --- a/target/executable/annotate/scanvi/.config.vsh.yaml +++ b/target/executable/annotate/scanvi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanvi" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -405,7 +405,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -442,11 +442,11 @@ build_info: output: "target/executable/annotate/scanvi" executable: "target/executable/annotate/scanvi/scanvi" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -476,7 +476,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/scanvi/scanvi b/target/executable/annotate/scanvi/scanvi index 88765d07..3ded4ccc 100755 --- a/target/executable/annotate/scanvi/scanvi +++ b/target/executable/annotate/scanvi/scanvi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scanvi v4.0.1 +# scanvi v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Jakub Majercik, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component annotate scanvi" -LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scanvi v4.0.1" + echo "scanvi v4.0.2" echo "" echo "scANVI () is a semi-supervised model for single-cell transcriptomics data." echo "scANVI is an scVI extension that can leverage the cell type knowledge for a" @@ -761,7 +761,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scanvi v4.0.1" + echo "scanvi v4.0.2" exit ;; --input) @@ -1117,7 +1117,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/scanvi:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/scanvi:v4.0.2' fi # print dockerfile diff --git a/target/executable/annotate/singler/.config.vsh.yaml b/target/executable/annotate/singler/.config.vsh.yaml index 3dde4793..79134993 100644 --- a/target/executable/annotate/singler/.config.vsh.yaml +++ b/target/executable/annotate/singler/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "singler" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -424,7 +424,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -483,11 +483,11 @@ build_info: output: "target/executable/annotate/singler" executable: "target/executable/annotate/singler/singler" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -517,7 +517,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/singler/singler b/target/executable/annotate/singler/singler index 738bcf61..26aee56b 100755 --- a/target/executable/annotate/singler/singler +++ b/target/executable/annotate/singler/singler @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# singler v4.0.1 +# singler v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -467,10 +467,10 @@ RUN pip install --user --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component annotate singler" -LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:18Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -587,7 +587,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "singler v4.0.1" + echo "singler v4.0.2" echo "" echo "SingleR performs reference-based cell type annotation for single-cell RNA-seq" echo "data" @@ -813,7 +813,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "singler v4.0.1" + echo "singler v4.0.2" exit ;; --input) @@ -1185,7 +1185,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/singler:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/singler:v4.0.2' fi # print dockerfile diff --git a/target/executable/annotate/svm_annotation/.config.vsh.yaml b/target/executable/annotate/svm_annotation/.config.vsh.yaml index 11940020..23cd7eb1 100644 --- a/target/executable/annotate/svm_annotation/.config.vsh.yaml +++ b/target/executable/annotate/svm_annotation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "svm_annotation" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -356,7 +356,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -403,11 +403,11 @@ build_info: output: "target/executable/annotate/svm_annotation" executable: "target/executable/annotate/svm_annotation/svm_annotation" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -437,7 +437,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/annotate/svm_annotation/svm_annotation b/target/executable/annotate/svm_annotation/svm_annotation index a3bd2ce3..89d9a49e 100755 --- a/target/executable/annotate/svm_annotation/svm_annotation +++ b/target/executable/annotate/svm_annotation/svm_annotation @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# svm_annotation v4.0.1 +# svm_annotation v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component annotate svm_annotation" -LABEL org.opencontainers.image.created="2026-02-04T09:06:24Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:18Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "svm_annotation v4.0.1" + echo "svm_annotation v4.0.2" echo "" echo "Automated cell type annotation tool for scRNA-seq datasets on the basis of SVMs." echo "" @@ -758,7 +758,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "svm_annotation v4.0.1" + echo "svm_annotation v4.0.2" exit ;; --input) @@ -1069,7 +1069,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/svm_annotation:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/annotate/svm_annotation:v4.0.2' fi # print dockerfile diff --git a/target/executable/cluster/leiden/.config.vsh.yaml b/target/executable/cluster/leiden/.config.vsh.yaml index 7c62be98..102e331b 100644 --- a/target/executable/cluster/leiden/.config.vsh.yaml +++ b/target/executable/cluster/leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "leiden" namespace: "cluster" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -215,7 +215,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -258,11 +258,11 @@ build_info: output: "target/executable/cluster/leiden" executable: "target/executable/cluster/leiden/leiden" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/cluster/leiden/leiden b/target/executable/cluster/leiden/leiden index 129be66d..5fcdc0fe 100755 --- a/target/executable/cluster/leiden/leiden +++ b/target/executable/cluster/leiden/leiden @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# leiden v4.0.1 +# leiden v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component cluster leiden" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "leiden v4.0.1" + echo "leiden v4.0.2" echo "" echo "Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy" echo "framework] [Wolf18]." @@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "leiden v4.0.1" + echo "leiden v4.0.2" exit ;; --input) @@ -871,7 +871,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/cluster/leiden:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/cluster/leiden:v4.0.2' fi # print dockerfile diff --git a/target/executable/compression/compress_h5mu/.config.vsh.yaml b/target/executable/compression/compress_h5mu/.config.vsh.yaml index ddd40b9e..038d3975 100644 --- a/target/executable/compression/compress_h5mu/.config.vsh.yaml +++ b/target/executable/compression/compress_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "compress_h5mu" namespace: "compression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -157,7 +157,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,11 @@ build_info: output: "target/executable/compression/compress_h5mu" executable: "target/executable/compression/compress_h5mu/compress_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -232,7 +232,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/compression/compress_h5mu/compress_h5mu b/target/executable/compression/compress_h5mu/compress_h5mu index 24d4fee6..39d63105 100755 --- a/target/executable/compression/compress_h5mu/compress_h5mu +++ b/target/executable/compression/compress_h5mu/compress_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# compress_h5mu v4.0.1 +# compress_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component compression compress_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "compress_h5mu v4.0.1" + echo "compress_h5mu v4.0.2" echo "" echo "Compress a MuData file." echo "" @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "compress_h5mu v4.0.1" + echo "compress_h5mu v4.0.2" exit ;; --input) @@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/compress_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/compress_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/compression/tar_extract/.config.vsh.yaml b/target/executable/compression/tar_extract/.config.vsh.yaml index 97bf9326..657fbf3a 100644 --- a/target/executable/compression/tar_extract/.config.vsh.yaml +++ b/target/executable/compression/tar_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tar_extract" namespace: "compression" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -157,7 +157,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -170,11 +170,11 @@ build_info: output: "target/executable/compression/tar_extract" executable: "target/executable/compression/tar_extract/tar_extract" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -204,7 +204,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/compression/tar_extract/tar_extract b/target/executable/compression/tar_extract/tar_extract index 21767fed..db7dc74f 100755 --- a/target/executable/compression/tar_extract/tar_extract +++ b/target/executable/compression/tar_extract/tar_extract @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tar_extract v4.0.1 +# tar_extract v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -446,10 +446,10 @@ function ViashDockerfile { FROM ubuntu:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component compression tar_extract" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -566,7 +566,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tar_extract v4.0.1" + echo "tar_extract v4.0.2" echo "" echo "Extract files from a tar archive" echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tar_extract v4.0.1" + echo "tar_extract v4.0.2" exit ;; --input) @@ -800,7 +800,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/tar_extract:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/compression/tar_extract:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml index b619ed53..a2c372a8 100644 --- a/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_10xh5_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_10xh5_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -263,7 +263,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -305,11 +305,11 @@ build_info: output: "target/executable/convert/from_10xh5_to_h5mu" executable: "target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -339,7 +339,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu b/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu index 31a6bae6..271898e3 100755 --- a/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu +++ b/target/executable/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_10xh5_to_h5mu v4.0.1 +# from_10xh5_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_10xh5_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_10xh5_to_h5mu v4.0.1" + echo "from_10xh5_to_h5mu v4.0.2" echo "" echo "Converts a 10x h5 into an h5mu file." echo "" @@ -669,7 +669,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_10xh5_to_h5mu v4.0.1" + echo "from_10xh5_to_h5mu v4.0.2" exit ;; --input) @@ -849,7 +849,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xh5_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xh5_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml index 4b539326..be938d47 100644 --- a/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_10xmtx_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_10xmtx_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -164,7 +164,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -206,11 +206,11 @@ build_info: output: "target/executable/convert/from_10xmtx_to_h5mu" executable: "target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -240,7 +240,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu b/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu index 35e46daf..d44ffeeb 100755 --- a/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu +++ b/target/executable/convert/from_10xmtx_to_h5mu/from_10xmtx_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_10xmtx_to_h5mu v4.0.1 +# from_10xmtx_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_10xmtx_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_10xmtx_to_h5mu v4.0.1" + echo "from_10xmtx_to_h5mu v4.0.2" echo "" echo "Converts a 10x mtx into an h5mu file." echo "" @@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_10xmtx_to_h5mu v4.0.1" + echo "from_10xmtx_to_h5mu v4.0.2" exit ;; --input) @@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xmtx_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_10xmtx_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml index 12a8c41e..e41a8ded 100644 --- a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml +++ b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_bd_to_10x_molecular_barcode_tags" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -161,7 +161,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -179,11 +179,11 @@ build_info: output: "target/executable/convert/from_bd_to_10x_molecular_barcode_tags" executable: "target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -213,7 +213,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags index b7c00199..a7cc463a 100755 --- a/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags +++ b/target/executable/convert/from_bd_to_10x_molecular_barcode_tags/from_bd_to_10x_molecular_barcode_tags @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_bd_to_10x_molecular_barcode_tags v4.0.1 +# from_bd_to_10x_molecular_barcode_tags v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_bd_to_10x_molecular_barcode_tags" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_bd_to_10x_molecular_barcode_tags v4.0.1" + echo "from_bd_to_10x_molecular_barcode_tags v4.0.2" echo "" echo "Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format" echo "(UB)." @@ -645,7 +645,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_bd_to_10x_molecular_barcode_tags v4.0.1" + echo "from_bd_to_10x_molecular_barcode_tags v4.0.2" exit ;; --input) @@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bd_to_10x_molecular_barcode_tags:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bd_to_10x_molecular_barcode_tags:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml index cc85b7e9..51095640 100644 --- a/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_bdrhap_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_bdrhap_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -190,7 +190,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -219,11 +219,11 @@ build_info: output: "target/executable/convert/from_bdrhap_to_h5mu" executable: "target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -253,7 +253,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu b/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu index b1612a27..174ee2b2 100755 --- a/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu +++ b/target/executable/convert/from_bdrhap_to_h5mu/from_bdrhap_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_bdrhap_to_h5mu v4.0.1 +# from_bdrhap_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_bdrhap_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_bdrhap_to_h5mu v4.0.1" + echo "from_bdrhap_to_h5mu v4.0.2" echo "" echo "Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file." echo "" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_bdrhap_to_h5mu v4.0.1" + echo "from_bdrhap_to_h5mu v4.0.2" exit ;; --output_compression) @@ -802,7 +802,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bdrhap_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_bdrhap_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml index 786bf15f..ebe2a628 100644 --- a/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_cellranger_multi_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -245,11 +245,11 @@ build_info: output: "target/executable/convert/from_cellranger_multi_to_h5mu" executable: "target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -279,7 +279,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu b/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu index e5573e21..69041f57 100755 --- a/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu +++ b/target/executable/convert/from_cellranger_multi_to_h5mu/from_cellranger_multi_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_cellranger_multi_to_h5mu v4.0.1 +# from_cellranger_multi_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_cellranger_multi_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_cellranger_multi_to_h5mu v4.0.1" + echo "from_cellranger_multi_to_h5mu v4.0.2" echo "" echo "Converts the output from cellranger multi to a single .h5mu file." echo "By default, will map the following library type names to modality names:" @@ -671,7 +671,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_cellranger_multi_to_h5mu v4.0.1" + echo "from_cellranger_multi_to_h5mu v4.0.2" exit ;; --input) @@ -829,7 +829,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_cellranger_multi_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_cellranger_multi_to_h5mu:v4.0.2' fi # print dockerfile @@ -1330,7 +1330,7 @@ def gather_input_data(dir: Path): found_input["count"] = dir feature_reference = found_input["count"] / "feature_reference.csv" - if feature_reference: + if feature_reference.is_file(): found_input["feature_reference"] = feature_reference per_sample_outs_dir = dir / "per_sample_outs" diff --git a/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml index bf363fa5..27463f52 100644 --- a/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_h5ad_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5ad_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -173,7 +173,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -214,11 +214,11 @@ build_info: output: "target/executable/convert/from_h5ad_to_h5mu" executable: "target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -248,7 +248,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu b/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu index 3d6183f2..a39e6dde 100755 --- a/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu +++ b/target/executable/convert/from_h5ad_to_h5mu/from_h5ad_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5ad_to_h5mu v4.0.1 +# from_h5ad_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5ad_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5ad_to_h5mu v4.0.1" + echo "from_h5ad_to_h5mu v4.0.2" echo "" echo "Converts a single layer h5ad file into a single MuData object" echo "" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5ad_to_h5mu v4.0.1" + echo "from_h5ad_to_h5mu v4.0.2" exit ;; --input) @@ -817,7 +817,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml b/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml index 33977900..1f1e10ac 100644 --- a/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml +++ b/target/executable/convert/from_h5ad_to_seurat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5ad_to_seurat" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -196,11 +196,11 @@ build_info: output: "target/executable/convert/from_h5ad_to_seurat" executable: "target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -230,7 +230,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat b/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat index 4b578a29..f6263d60 100755 --- a/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat +++ b/target/executable/convert/from_h5ad_to_seurat/from_h5ad_to_seurat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5ad_to_seurat v4.0.1 +# from_h5ad_to_seurat v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN RUN Rscript -e 'options(warn = 2); remotes::install_github(c("scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5ad_to_seurat" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5ad_to_seurat v4.0.1" + echo "from_h5ad_to_seurat v4.0.2" echo "" echo "Converts an h5ad file into a Seurat file." echo "" @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5ad_to_seurat v4.0.1" + echo "from_h5ad_to_seurat v4.0.2" exit ;; --input) @@ -782,7 +782,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_seurat:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5ad_to_seurat:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml index a1358a6d..6b22af5c 100644 --- a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml +++ b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_or_h5ad_to_seurat" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -166,7 +166,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -205,11 +205,11 @@ build_info: output: "target/executable/convert/from_h5mu_or_h5ad_to_seurat" executable: "target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -239,7 +239,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat index a7dfaf68..0a63b3d9 100755 --- a/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat +++ b/target/executable/convert/from_h5mu_or_h5ad_to_seurat/from_h5mu_or_h5ad_to_seurat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5mu_or_h5ad_to_seurat v4.0.1 +# from_h5mu_or_h5ad_to_seurat v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN RUN Rscript -e 'options(warn = 2); remotes::install_github(c("scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_or_h5ad_to_seurat" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5mu_or_h5ad_to_seurat v4.0.1" + echo "from_h5mu_or_h5ad_to_seurat v4.0.2" echo "" echo "Converts an h5ad file or a single modality of an h5mu file into a Seurat file." echo "" @@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5mu_or_h5ad_to_seurat v4.0.1" + echo "from_h5mu_or_h5ad_to_seurat v4.0.2" exit ;; --input) @@ -798,7 +798,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_seurat:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_seurat:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml index be87fab4..1a295fc0 100644 --- a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml +++ b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_or_h5ad_to_tiledb" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -334,7 +334,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -381,11 +381,11 @@ build_info: output: "target/executable/convert/from_h5mu_or_h5ad_to_tiledb" executable: "target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -415,7 +415,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb index 35ee8654..b5e9dddc 100755 --- a/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb +++ b/target/executable/convert/from_h5mu_or_h5ad_to_tiledb/from_h5mu_or_h5ad_to_tiledb @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5mu_or_h5ad_to_tiledb v4.0.1 +# from_h5mu_or_h5ad_to_tiledb v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_or_h5ad_to_tiledb" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5mu_or_h5ad_to_tiledb v4.0.1" + echo "from_h5mu_or_h5ad_to_tiledb v4.0.2" echo "" echo "Convert a MuData or AnnData object to tiledb. Currently, transcriptome and" echo "protein modalities are supported." @@ -747,7 +747,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5mu_or_h5ad_to_tiledb v4.0.1" + echo "from_h5mu_or_h5ad_to_tiledb v4.0.2" exit ;; --input) @@ -1047,7 +1047,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_tiledb:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_or_h5ad_to_tiledb:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml index 7544b982..6e79fa3c 100644 --- a/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml +++ b/target/executable/convert/from_h5mu_to_h5ad/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_to_h5ad" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -174,7 +174,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -215,11 +215,11 @@ build_info: output: "target/executable/convert/from_h5mu_to_h5ad" executable: "target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -249,7 +249,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad b/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad index e66c4e7d..34ef9436 100755 --- a/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad +++ b/target/executable/convert/from_h5mu_to_h5ad/from_h5mu_to_h5ad @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5mu_to_h5ad v4.0.1 +# from_h5mu_to_h5ad v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_h5ad" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5mu_to_h5ad v4.0.1" + echo "from_h5mu_to_h5ad v4.0.2" echo "" echo "Converts a h5mu file into a h5ad file." echo "" @@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5mu_to_h5ad v4.0.1" + echo "from_h5mu_to_h5ad v4.0.2" exit ;; --input) @@ -799,7 +799,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_h5ad:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_h5ad:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml index d659bd9e..32835e9b 100644 --- a/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml +++ b/target/executable/convert/from_h5mu_to_seurat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_to_seurat" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -155,7 +155,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -188,11 +188,11 @@ build_info: output: "target/executable/convert/from_h5mu_to_seurat" executable: "target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -222,7 +222,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat b/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat index afff4690..10061d7c 100755 --- a/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat +++ b/target/executable/convert/from_h5mu_to_seurat/from_h5mu_to_seurat @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_h5mu_to_seurat v4.0.1 +# from_h5mu_to_seurat v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN RUN Rscript -e 'options(warn = 2); remotes::install_github(c("pmbio/MuDataSeurat@empty-tables-and-nullable"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_seurat" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_h5mu_to_seurat v4.0.1" + echo "from_h5mu_to_seurat v4.0.2" echo "" echo "Converts an h5mu file into a Seurat file." echo "" @@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_h5mu_to_seurat v4.0.1" + echo "from_h5mu_to_seurat v4.0.2" exit ;; --input) @@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_seurat:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_h5mu_to_seurat:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml index 605c01ce..83dae9a1 100644 --- a/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_seurat_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_seurat_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -312,7 +312,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -388,11 +388,11 @@ build_info: output: "target/executable/convert/from_seurat_to_h5mu" executable: "target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -422,7 +422,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu b/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu index 2c9d0ecf..6d698e1e 100755 --- a/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu +++ b/target/executable/convert/from_seurat_to_h5mu/from_seurat_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_seurat_to_h5mu v4.0.1 +# from_seurat_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -472,10 +472,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_seurat_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -592,7 +592,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_seurat_to_h5mu v4.0.1" + echo "from_seurat_to_h5mu v4.0.2" echo "" echo "Converts a Seurat file into an H5MU file." echo "" @@ -758,7 +758,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_seurat_to_h5mu v4.0.1" + echo "from_seurat_to_h5mu v4.0.2" exit ;; --input) @@ -1015,7 +1015,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_seurat_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_seurat_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml index 2f9d4df8..776d9b43 100644 --- a/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_tiledb_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_tiledb_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -214,7 +214,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -258,11 +258,11 @@ build_info: output: "target/executable/convert/from_tiledb_to_h5mu" executable: "target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu b/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu index ebd2551b..5b9fe4c4 100755 --- a/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu +++ b/target/executable/convert/from_tiledb_to_h5mu/from_tiledb_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# from_tiledb_to_h5mu v4.0.1 +# from_tiledb_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component convert from_tiledb_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env AWS_ACCESS_KEY_ID --env AWS_SECRET_ACCESS_K # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "from_tiledb_to_h5mu v4.0.1" + echo "from_tiledb_to_h5mu v4.0.2" echo "" echo "Input database:" echo " Open a tileDB-SOMA database by URI." @@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "from_tiledb_to_h5mu v4.0.1" + echo "from_tiledb_to_h5mu v4.0.2" exit ;; --input_uri) @@ -866,7 +866,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_tiledb_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/from_tiledb_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml index f54750d6..60e9530e 100644 --- a/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/velocyto_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "velocyto_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -244,7 +244,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -275,11 +275,11 @@ build_info: output: "target/executable/convert/velocyto_to_h5mu" executable: "target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -309,7 +309,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu b/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu index 304ea347..0b013b23 100755 --- a/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu +++ b/target/executable/convert/velocyto_to_h5mu/velocyto_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# velocyto_to_h5mu v4.0.1 +# velocyto_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -460,10 +460,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component convert velocyto_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -580,7 +580,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "velocyto_to_h5mu v4.0.1" + echo "velocyto_to_h5mu v4.0.2" echo "" echo "Convert a velocyto loom file to a h5mu file." echo "" @@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "velocyto_to_h5mu v4.0.1" + echo "velocyto_to_h5mu v4.0.2" exit ;; --input_loom) @@ -857,7 +857,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/velocyto_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/convert/velocyto_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/correction/cellbender_remove_background/.config.vsh.yaml b/target/executable/correction/cellbender_remove_background/.config.vsh.yaml index a4ef0c81..cdd29eb3 100644 --- a/target/executable/correction/cellbender_remove_background/.config.vsh.yaml +++ b/target/executable/correction/cellbender_remove_background/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellbender_remove_background" namespace: "correction" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Inputs" arguments: @@ -578,7 +578,7 @@ engines: id: "docker" image: "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -611,11 +611,11 @@ build_info: output: "target/executable/correction/cellbender_remove_background" executable: "target/executable/correction/cellbender_remove_background/cellbender_remove_background" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -645,7 +645,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/correction/cellbender_remove_background/cellbender_remove_background b/target/executable/correction/cellbender_remove_background/cellbender_remove_background index 36506005..6d4c8f88 100755 --- a/target/executable/correction/cellbender_remove_background/cellbender_remove_background +++ b/target/executable/correction/cellbender_remove_background/cellbender_remove_background @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellbender_remove_background v4.0.1 +# cellbender_remove_background v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "lxml~=4.8.0" "mudata~=0.2.1" "cellbender~=0.3.0" LABEL org.opencontainers.image.description="Companion container for running component correction cellbender_remove_background" -LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellbender_remove_background v4.0.1" + echo "cellbender_remove_background v4.0.2" echo "" echo "Eliminating technical artifacts from high-throughput single-cell RNA sequencing" echo "data." @@ -911,7 +911,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellbender_remove_background v4.0.1" + echo "cellbender_remove_background v4.0.2" exit ;; --input) @@ -1482,7 +1482,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/correction/cellbender_remove_background:v4.0.2' fi # print dockerfile diff --git a/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml index ba36467a..7595c9c8 100644 --- a/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml +++ b/target/executable/dataflow/concatenate_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "concatenate_h5mu" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -253,7 +253,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -300,11 +300,11 @@ build_info: output: "target/executable/dataflow/concatenate_h5mu" executable: "target/executable/dataflow/concatenate_h5mu/concatenate_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -334,7 +334,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu b/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu index 83f5be2c..b394c3b7 100755 --- a/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu +++ b/target/executable/dataflow/concatenate_h5mu/concatenate_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# concatenate_h5mu v4.0.1 +# concatenate_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow concatenate_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "concatenate_h5mu v4.0.1" + echo "concatenate_h5mu v4.0.2" echo "" echo "Concatenate observations from samples in several (uni- and/or multi-modal)" echo "MuData files into a single file." @@ -706,7 +706,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "concatenate_h5mu v4.0.1" + echo "concatenate_h5mu v4.0.2" exit ;; --input) @@ -935,7 +935,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/concatenate_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/concatenate_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/dataflow/merge/.config.vsh.yaml b/target/executable/dataflow/merge/.config.vsh.yaml index 3b0ba162..990bfdcf 100644 --- a/target/executable/dataflow/merge/.config.vsh.yaml +++ b/target/executable/dataflow/merge/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "merge" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -163,7 +163,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -204,11 +204,11 @@ build_info: output: "target/executable/dataflow/merge" executable: "target/executable/dataflow/merge/merge" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -238,7 +238,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dataflow/merge/merge b/target/executable/dataflow/merge/merge index 952a7606..4470d129 100755 --- a/target/executable/dataflow/merge/merge +++ b/target/executable/dataflow/merge/merge @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# merge v4.0.1 +# merge v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component dataflow merge" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "merge v4.0.1" + echo "merge v4.0.2" echo "" echo "Combine one or more single-modality .h5mu files together into one .h5mu file." echo "" @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "merge v4.0.1" + echo "merge v4.0.2" exit ;; --input) @@ -791,7 +791,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/merge:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/merge:v4.0.2' fi # print dockerfile diff --git a/target/executable/dataflow/split_h5mu/.config.vsh.yaml b/target/executable/dataflow/split_h5mu/.config.vsh.yaml index e01ec4d2..f49e17fa 100644 --- a/target/executable/dataflow/split_h5mu/.config.vsh.yaml +++ b/target/executable/dataflow/split_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_h5mu" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -203,7 +203,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -244,11 +244,11 @@ build_info: output: "target/executable/dataflow/split_h5mu" executable: "target/executable/dataflow/split_h5mu/split_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -278,7 +278,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dataflow/split_h5mu/split_h5mu b/target/executable/dataflow/split_h5mu/split_h5mu index 3f9e2a24..907541ba 100755 --- a/target/executable/dataflow/split_h5mu/split_h5mu +++ b/target/executable/dataflow/split_h5mu/split_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# split_h5mu v4.0.1 +# split_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component dataflow split_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "split_h5mu v4.0.1" + echo "split_h5mu v4.0.2" echo "" echo "Split the samples of a single modality from a .h5mu (multimodal) sample into" echo "seperate .h5mu files based on the values of an .obs column of this modality." @@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "split_h5mu v4.0.1" + echo "split_h5mu v4.0.2" exit ;; --input) @@ -841,7 +841,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/dataflow/split_modalities/.config.vsh.yaml b/target/executable/dataflow/split_modalities/.config.vsh.yaml index 733317f9..9ad7b179 100644 --- a/target/executable/dataflow/split_modalities/.config.vsh.yaml +++ b/target/executable/dataflow/split_modalities/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_modalities" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -190,7 +190,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -231,11 +231,11 @@ build_info: output: "target/executable/dataflow/split_modalities" executable: "target/executable/dataflow/split_modalities/split_modalities" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -265,7 +265,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dataflow/split_modalities/split_modalities b/target/executable/dataflow/split_modalities/split_modalities index 420957ee..678b098c 100755 --- a/target/executable/dataflow/split_modalities/split_modalities +++ b/target/executable/dataflow/split_modalities/split_modalities @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# split_modalities v4.0.1 +# split_modalities v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component dataflow split_modalities" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:05Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "split_modalities v4.0.1" + echo "split_modalities v4.0.2" echo "" echo "Split the modalities from a single .h5mu multimodal sample into seperate .h5mu" echo "files." @@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "split_modalities v4.0.1" + echo "split_modalities v4.0.2" exit ;; --input) @@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_modalities:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dataflow/split_modalities:v4.0.2' fi # print dockerfile diff --git a/target/executable/demux/bcl2fastq/.config.vsh.yaml b/target/executable/demux/bcl2fastq/.config.vsh.yaml index d0c9e831..02f260c6 100644 --- a/target/executable/demux/bcl2fastq/.config.vsh.yaml +++ b/target/executable/demux/bcl2fastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcl2fastq" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Toni Verbeiren" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/bcl2fastq:2.20" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -196,11 +196,11 @@ build_info: output: "target/executable/demux/bcl2fastq" executable: "target/executable/demux/bcl2fastq/bcl2fastq" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -230,7 +230,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/demux/bcl2fastq/bcl2fastq b/target/executable/demux/bcl2fastq/bcl2fastq index 2306e871..bda9eeb5 100755 --- a/target/executable/demux/bcl2fastq/bcl2fastq +++ b/target/executable/demux/bcl2fastq/bcl2fastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcl2fastq v4.0.1 +# bcl2fastq v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component demux bcl2fastq" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcl2fastq v4.0.1" + echo "bcl2fastq v4.0.2" echo "" echo "Convert bcl files to fastq files using bcl2fastq." echo "" @@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcl2fastq v4.0.1" + echo "bcl2fastq v4.0.2" exit ;; --input) @@ -816,7 +816,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl2fastq:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl2fastq:v4.0.2' fi # print dockerfile diff --git a/target/executable/demux/bcl_convert/.config.vsh.yaml b/target/executable/demux/bcl_convert/.config.vsh.yaml index 564dc106..be3963b3 100644 --- a/target/executable/demux/bcl_convert/.config.vsh.yaml +++ b/target/executable/demux/bcl_convert/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcl_convert" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Toni Verbeiren" roles: @@ -250,7 +250,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/bclconvert:4.2" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -268,11 +268,11 @@ build_info: output: "target/executable/demux/bcl_convert" executable: "target/executable/demux/bcl_convert/bcl_convert" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -302,7 +302,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/demux/bcl_convert/bcl_convert b/target/executable/demux/bcl_convert/bcl_convert index b966fa21..da18f7d8 100755 --- a/target/executable/demux/bcl_convert/bcl_convert +++ b/target/executable/demux/bcl_convert/bcl_convert @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcl_convert v4.0.1 +# bcl_convert v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Toni Verbeiren, Marijke Van Moerbeke, Weiwei Schultz, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component demux bcl_convert" -LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcl_convert v4.0.1" + echo "bcl_convert v4.0.2" echo "" echo "Convert bcl files to fastq files using bcl-convert." echo "Information about upgrading from bcl2fastq via" @@ -675,7 +675,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcl_convert v4.0.1" + echo "bcl_convert v4.0.2" exit ;; --input) @@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl_convert:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/bcl_convert:v4.0.2' fi # print dockerfile diff --git a/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml b/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml index c205fdd8..9e42cfe7 100644 --- a/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml +++ b/target/executable/demux/cellranger_atac_mkfastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_atac_mkfastq" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -213,7 +213,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger_atac:2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -237,11 +237,11 @@ build_info: output: "target/executable/demux/cellranger_atac_mkfastq" executable: "target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -271,7 +271,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq b/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq index bc312260..544f04df 100755 --- a/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq +++ b/target/executable/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_atac_mkfastq v4.0.1 +# cellranger_atac_mkfastq v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ RUN DEBIAN_FRONTEND=noninteractive apt update \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component demux cellranger_atac_mkfastq" -LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_atac_mkfastq v4.0.1" + echo "cellranger_atac_mkfastq v4.0.2" echo "" echo "Demultiplex raw sequencing data for ATAC experiments" echo "" @@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_atac_mkfastq v4.0.1" + echo "cellranger_atac_mkfastq v4.0.2" exit ;; --input) @@ -863,7 +863,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_atac_mkfastq:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_atac_mkfastq:v4.0.2' fi # print dockerfile diff --git a/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml b/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml index 93fff20f..b0b88d97 100644 --- a/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml +++ b/target/executable/demux/cellranger_mkfastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mkfastq" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -204,7 +204,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -228,11 +228,11 @@ build_info: output: "target/executable/demux/cellranger_mkfastq" executable: "target/executable/demux/cellranger_mkfastq/cellranger_mkfastq" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -262,7 +262,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq b/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq index 21119d46..07cc71be 100755 --- a/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq +++ b/target/executable/demux/cellranger_mkfastq/cellranger_mkfastq @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_mkfastq v4.0.1 +# cellranger_mkfastq v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component demux cellranger_mkfastq" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_mkfastq v4.0.1" + echo "cellranger_mkfastq v4.0.2" echo "" echo "Demultiplex raw sequencing data" echo "" @@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_mkfastq v4.0.1" + echo "cellranger_mkfastq v4.0.2" exit ;; --input) @@ -789,7 +789,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_mkfastq:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/demux/cellranger_mkfastq:v4.0.2' fi # print dockerfile diff --git a/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml b/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml index 183eb61f..6aff9681 100644 --- a/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml +++ b/target/executable/differential_expression/create_pseudobulk/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pseudobulk" namespace: "differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -271,7 +271,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -309,11 +309,11 @@ build_info: output: "target/executable/differential_expression/create_pseudobulk" executable: "target/executable/differential_expression/create_pseudobulk/create_pseudobulk" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -343,7 +343,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/differential_expression/create_pseudobulk/create_pseudobulk b/target/executable/differential_expression/create_pseudobulk/create_pseudobulk index 043326a4..239cc36f 100755 --- a/target/executable/differential_expression/create_pseudobulk/create_pseudobulk +++ b/target/executable/differential_expression/create_pseudobulk/create_pseudobulk @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_pseudobulk v4.0.1 +# create_pseudobulk v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Jakub Majercik, Dries De Maeyer, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component differential_expression create_pseudobulk" -LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pseudobulk v4.0.1" + echo "create_pseudobulk v4.0.2" echo "" echo "Generation of pseudobulk samples from single-cell transcriptomics data," echo "by aggregating raw gene expression counts from individual cells to create" @@ -689,7 +689,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pseudobulk v4.0.1" + echo "create_pseudobulk v4.0.2" exit ;; --input) @@ -902,7 +902,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/create_pseudobulk:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/create_pseudobulk:v4.0.2' fi # print dockerfile diff --git a/target/executable/differential_expression/deseq2/.config.vsh.yaml b/target/executable/differential_expression/deseq2/.config.vsh.yaml index 879a2327..b855a1be 100644 --- a/target/executable/differential_expression/deseq2/.config.vsh.yaml +++ b/target/executable/differential_expression/deseq2/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "deseq2" namespace: "differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -294,7 +294,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -346,11 +346,11 @@ build_info: output: "target/executable/differential_expression/deseq2" executable: "target/executable/differential_expression/deseq2/deseq2" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -380,7 +380,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/differential_expression/deseq2/deseq2 b/target/executable/differential_expression/deseq2/deseq2 index 2547d01f..b37c8ad4 100755 --- a/target/executable/differential_expression/deseq2/deseq2 +++ b/target/executable/differential_expression/deseq2/deseq2 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# deseq2 v4.0.1 +# deseq2 v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -464,10 +464,10 @@ RUN --mount=type=secret,id=GITHUB_TOKEN,env=GITHUB_TOKEN RUN Rscript -e 'options(warn = 2); remotes::install_github(c("scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.authors="Jakub Majercik, Dorien Roosen, Dries De Maeyer, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component differential_expression deseq2" -LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -584,7 +584,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "deseq2 v4.0.1" + echo "deseq2 v4.0.2" echo "" echo "Performs differential expression analysis using DESeq2 on bulk samples or" echo "pseudobulk samples aggregated from single-cell data." @@ -724,7 +724,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "deseq2 v4.0.1" + echo "deseq2 v4.0.2" exit ;; --input) @@ -965,7 +965,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/deseq2:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/differential_expression/deseq2:v4.0.2' fi # print dockerfile diff --git a/target/executable/dimred/densmap/.config.vsh.yaml b/target/executable/dimred/densmap/.config.vsh.yaml index 8a880202..117a92c1 100644 --- a/target/executable/dimred/densmap/.config.vsh.yaml +++ b/target/executable/dimred/densmap/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "densmap" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -353,7 +353,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -395,11 +395,11 @@ build_info: output: "target/executable/dimred/densmap" executable: "target/executable/dimred/densmap/densmap" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -429,7 +429,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dimred/densmap/densmap b/target/executable/dimred/densmap/densmap index 959a07e2..df457f34 100755 --- a/target/executable/dimred/densmap/densmap +++ b/target/executable/dimred/densmap/densmap @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# densmap v4.0.1 +# densmap v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component dimred densmap" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "densmap v4.0.1" + echo "densmap v4.0.2" echo "" echo "A modification of UMAP that adds an extra cost term in order to preserve" echo "information" @@ -774,7 +774,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "densmap v4.0.1" + echo "densmap v4.0.2" exit ;; --input) @@ -1069,7 +1069,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/densmap:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/densmap:v4.0.2' fi # print dockerfile diff --git a/target/executable/dimred/lsi/.config.vsh.yaml b/target/executable/dimred/lsi/.config.vsh.yaml index 02348afa..50dd13d5 100644 --- a/target/executable/dimred/lsi/.config.vsh.yaml +++ b/target/executable/dimred/lsi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lsi" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Sarah Ouologuem" roles: @@ -269,7 +269,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -314,11 +314,11 @@ build_info: output: "target/executable/dimred/lsi" executable: "target/executable/dimred/lsi/lsi" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -348,7 +348,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dimred/lsi/lsi b/target/executable/dimred/lsi/lsi index f7b4d0d0..fef037c4 100755 --- a/target/executable/dimred/lsi/lsi +++ b/target/executable/dimred/lsi/lsi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# lsi v4.0.1 +# lsi v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Sarah Ouologuem, Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component dimred lsi" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lsi v4.0.1" + echo "lsi v4.0.2" echo "" echo "Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and" echo "singular values. Uses the implementation of scipy." @@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lsi v4.0.1" + echo "lsi v4.0.2" exit ;; --input) @@ -925,7 +925,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/lsi:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/lsi:v4.0.2' fi # print dockerfile diff --git a/target/executable/dimred/pca/.config.vsh.yaml b/target/executable/dimred/pca/.config.vsh.yaml index 00d25f73..a4f14828 100644 --- a/target/executable/dimred/pca/.config.vsh.yaml +++ b/target/executable/dimred/pca/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pca" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -240,7 +240,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -276,11 +276,11 @@ build_info: output: "target/executable/dimred/pca" executable: "target/executable/dimred/pca/pca" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -310,7 +310,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dimred/pca/pca b/target/executable/dimred/pca/pca index d165424b..c0f0d6a3 100755 --- a/target/executable/dimred/pca/pca +++ b/target/executable/dimred/pca/pca @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# pca v4.0.1 +# pca v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component dimred pca" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "pca v4.0.1" + echo "pca v4.0.2" echo "" echo "Computes PCA coordinates, loadings and variance decomposition. Uses the" echo "implementation of scikit-learn [Pedregosa11]." @@ -689,7 +689,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pca v4.0.1" + echo "pca v4.0.2" exit ;; --input) @@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/pca:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/pca:v4.0.2' fi # print dockerfile diff --git a/target/executable/dimred/tsne/.config.vsh.yaml b/target/executable/dimred/tsne/.config.vsh.yaml index 9147ac2c..3aefc6a4 100644 --- a/target/executable/dimred/tsne/.config.vsh.yaml +++ b/target/executable/dimred/tsne/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tsne" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -281,7 +281,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -323,11 +323,11 @@ build_info: output: "target/executable/dimred/tsne" executable: "target/executable/dimred/tsne/tsne" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -357,7 +357,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dimred/tsne/tsne b/target/executable/dimred/tsne/tsne index 6cf4839d..bf0ceb86 100755 --- a/target/executable/dimred/tsne/tsne +++ b/target/executable/dimred/tsne/tsne @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tsne v4.0.1 +# tsne v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component dimred tsne" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tsne v4.0.1" + echo "tsne v4.0.2" echo "" echo "t-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality" echo "reduction technique used to visualize high-dimensional data in a low-dimensional" @@ -715,7 +715,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tsne v4.0.1" + echo "tsne v4.0.2" exit ;; --input) @@ -955,7 +955,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/tsne:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/tsne:v4.0.2' fi # print dockerfile diff --git a/target/executable/dimred/umap/.config.vsh.yaml b/target/executable/dimred/umap/.config.vsh.yaml index 444f5a08..eb942e34 100644 --- a/target/executable/dimred/umap/.config.vsh.yaml +++ b/target/executable/dimred/umap/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umap" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -294,7 +294,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -330,11 +330,11 @@ build_info: output: "target/executable/dimred/umap" executable: "target/executable/dimred/umap/umap" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -364,7 +364,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/dimred/umap/umap b/target/executable/dimred/umap/umap index dbf9883b..cb4d4c00 100755 --- a/target/executable/dimred/umap/umap +++ b/target/executable/dimred/umap/umap @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# umap v4.0.1 +# umap v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component dimred umap" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:20Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "umap v4.0.1" + echo "umap v4.0.2" echo "" echo "UMAP (Uniform Manifold Approximation and Projection) is a manifold learning" echo "technique suitable for visualizing high-dimensional data. Besides tending to be" @@ -726,7 +726,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umap v4.0.1" + echo "umap v4.0.2" exit ;; --input) @@ -977,7 +977,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/umap:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/dimred/umap:v4.0.2' fi # print dockerfile diff --git a/target/executable/download/download_file/.config.vsh.yaml b/target/executable/download/download_file/.config.vsh.yaml index 68f75e5d..f4af5497 100644 --- a/target/executable/download/download_file/.config.vsh.yaml +++ b/target/executable/download/download_file/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "download_file" namespace: "download" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -146,7 +146,7 @@ engines: id: "docker" image: "bash:5.1.16" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -159,11 +159,11 @@ build_info: output: "target/executable/download/download_file" executable: "target/executable/download/download_file/download_file" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -193,7 +193,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/download/download_file/download_file b/target/executable/download/download_file/download_file index 69ba5b3b..7ec6b8c8 100755 --- a/target/executable/download/download_file/download_file +++ b/target/executable/download/download_file/download_file @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# download_file v4.0.1 +# download_file v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ FROM bash:5.1.16 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component download download_file" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "download_file v4.0.1" + echo "download_file v4.0.2" echo "" echo "Download a file." echo "" @@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "download_file v4.0.1" + echo "download_file v4.0.2" exit ;; --input) @@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/download_file:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/download/download_file:v4.0.2' fi # print dockerfile diff --git a/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml b/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml index 9f3d977d..6b5fa1f9 100644 --- a/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml +++ b/target/executable/feature_annotation/align_query_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "align_query_reference" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -476,7 +476,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -517,11 +517,11 @@ build_info: output: "target/executable/feature_annotation/align_query_reference" executable: "target/executable/feature_annotation/align_query_reference/align_query_reference" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -551,7 +551,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/feature_annotation/align_query_reference/align_query_reference b/target/executable/feature_annotation/align_query_reference/align_query_reference index 47be917f..f1de3771 100755 --- a/target/executable/feature_annotation/align_query_reference/align_query_reference +++ b/target/executable/feature_annotation/align_query_reference/align_query_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# align_query_reference v4.0.1 +# align_query_reference v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation align_query_reference" -LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "align_query_reference v4.0.1" + echo "align_query_reference v4.0.2" echo "" echo "Alignment of a query and reference dataset by:" echo "* Alignment of layers" @@ -835,7 +835,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "align_query_reference v4.0.1" + echo "align_query_reference v4.0.2" exit ;; --input) @@ -1260,7 +1260,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/align_query_reference:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/align_query_reference:v4.0.2' fi # print dockerfile diff --git a/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml index f3f1a771..0ef4449f 100644 --- a/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml +++ b/target/executable/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "highly_variable_features_scanpy" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -342,7 +342,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -381,11 +381,11 @@ build_info: output: "target/executable/feature_annotation/highly_variable_features_scanpy" executable: "target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -415,7 +415,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy b/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy index b056d069..8c319d60 100755 --- a/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy +++ b/target/executable/feature_annotation/highly_variable_features_scanpy/highly_variable_features_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# highly_variable_features_scanpy v4.0.1 +# highly_variable_features_scanpy v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation highly_variable_features_scanpy" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "highly_variable_features_scanpy v4.0.1" + echo "highly_variable_features_scanpy v4.0.2" echo "" echo "Annotate highly variable features [Satija15] [Zheng17] [Stuart19]." echo "" @@ -753,7 +753,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "highly_variable_features_scanpy v4.0.1" + echo "highly_variable_features_scanpy v4.0.2" exit ;; --input) @@ -1031,7 +1031,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/highly_variable_features_scanpy:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/highly_variable_features_scanpy:v4.0.2' fi # print dockerfile diff --git a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml index 0959d0e5..10b25bae 100644 --- a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml +++ b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "score_genes_cell_cycle_scanpy" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -367,7 +367,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -399,11 +399,11 @@ build_info: output: "target/executable/feature_annotation/score_genes_cell_cycle_scanpy" executable: "target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -433,7 +433,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy index dc158e3e..2baba378 100755 --- a/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy +++ b/target/executable/feature_annotation/score_genes_cell_cycle_scanpy/score_genes_cell_cycle_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# score_genes_cell_cycle_scanpy v4.0.1 +# score_genes_cell_cycle_scanpy v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -456,10 +456,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation score_genes_cell_cycle_scanpy" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "score_genes_cell_cycle_scanpy v4.0.1" + echo "score_genes_cell_cycle_scanpy v4.0.2" echo "" echo "Calculates the score associated to S phase and G2M phase and annotates the cell" echo "cycle phase for each cell, as implemented by scanpy." @@ -748,7 +748,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "score_genes_cell_cycle_scanpy v4.0.1" + echo "score_genes_cell_cycle_scanpy v4.0.2" exit ;; --input) @@ -1055,7 +1055,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_cell_cycle_scanpy:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_cell_cycle_scanpy:v4.0.2' fi # print dockerfile diff --git a/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml b/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml index 49181863..bb58ad91 100644 --- a/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml +++ b/target/executable/feature_annotation/score_genes_scanpy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "score_genes_scanpy" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -256,7 +256,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -288,11 +288,11 @@ build_info: output: "target/executable/feature_annotation/score_genes_scanpy" executable: "target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -322,7 +322,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy b/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy index ee844f33..b60dd507 100755 --- a/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy +++ b/target/executable/feature_annotation/score_genes_scanpy/score_genes_scanpy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# score_genes_scanpy v4.0.1 +# score_genes_scanpy v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -456,10 +456,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component feature_annotation score_genes_scanpy" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "score_genes_scanpy v4.0.1" + echo "score_genes_scanpy v4.0.2" echo "" echo "Calculates the score of a set of genes for each cell, as implemented by scanpy." echo "The score is the average expression of a set of genes subtracted with the" @@ -719,7 +719,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "score_genes_scanpy v4.0.1" + echo "score_genes_scanpy v4.0.2" exit ;; --input) @@ -987,7 +987,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_scanpy:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/feature_annotation/score_genes_scanpy:v4.0.2' fi # print dockerfile diff --git a/target/executable/files/make_params/.config.vsh.yaml b/target/executable/files/make_params/.config.vsh.yaml index 557a637e..e04c9164 100644 --- a/target/executable/files/make_params/.config.vsh.yaml +++ b/target/executable/files/make_params/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "make_params" namespace: "files" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -223,7 +223,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/randpy:r4.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -236,11 +236,11 @@ build_info: output: "target/executable/files/make_params" executable: "target/executable/files/make_params/make_params" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -270,7 +270,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/files/make_params/make_params b/target/executable/files/make_params/make_params index 6c254f7d..46275015 100755 --- a/target/executable/files/make_params/make_params +++ b/target/executable/files/make_params/make_params @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# make_params v4.0.1 +# make_params v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -451,10 +451,10 @@ FROM ghcr.io/data-intuitive/randpy:r4.0 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component files make_params" -LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -571,7 +571,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "make_params v4.0.1" + echo "make_params v4.0.2" echo "" echo "Looks for files in a directory and turn it in a params file." echo "" @@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "make_params v4.0.1" + echo "make_params v4.0.2" exit ;; --base_dir) @@ -843,7 +843,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/files/make_params:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/files/make_params:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/delimit_fraction/.config.vsh.yaml b/target/executable/filter/delimit_fraction/.config.vsh.yaml index fd99c482..67c33e4f 100644 --- a/target/executable/filter/delimit_fraction/.config.vsh.yaml +++ b/target/executable/filter/delimit_fraction/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "delimit_fraction" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -219,7 +219,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -260,11 +260,11 @@ build_info: output: "target/executable/filter/delimit_fraction" executable: "target/executable/filter/delimit_fraction/delimit_fraction" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -294,7 +294,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/delimit_fraction/delimit_fraction b/target/executable/filter/delimit_fraction/delimit_fraction index f3f2ce13..b027b6ec 100755 --- a/target/executable/filter/delimit_fraction/delimit_fraction +++ b/target/executable/filter/delimit_fraction/delimit_fraction @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# delimit_fraction v4.0.1 +# delimit_fraction v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter delimit_fraction" -LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:15Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "delimit_fraction v4.0.1" + echo "delimit_fraction v4.0.2" echo "" echo "Turns a column containing values between 0 and 1 into a boolean column based on" echo "thresholds." @@ -680,7 +680,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "delimit_fraction v4.0.1" + echo "delimit_fraction v4.0.2" exit ;; --input) @@ -859,7 +859,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_fraction:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/delimit_fraction:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/do_filter/.config.vsh.yaml b/target/executable/filter/do_filter/.config.vsh.yaml index 3735fca7..00256d77 100644 --- a/target/executable/filter/do_filter/.config.vsh.yaml +++ b/target/executable/filter/do_filter/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "do_filter" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -193,7 +193,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -228,11 +228,11 @@ build_info: output: "target/executable/filter/do_filter" executable: "target/executable/filter/do_filter/do_filter" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -262,7 +262,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/do_filter/do_filter b/target/executable/filter/do_filter/do_filter index 4b618db6..6a6a56cf 100755 --- a/target/executable/filter/do_filter/do_filter +++ b/target/executable/filter/do_filter/do_filter @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# do_filter v4.0.1 +# do_filter v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter do_filter" -LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:15Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "do_filter v4.0.1" + echo "do_filter v4.0.2" echo "" echo "Remove observations and variables based on specified .obs and .var columns." echo "" @@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "do_filter v4.0.1" + echo "do_filter v4.0.2" exit ;; --input) @@ -831,7 +831,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/do_filter:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/do_filter:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/filter_with_counts/.config.vsh.yaml b/target/executable/filter/filter_with_counts/.config.vsh.yaml index 49262043..94a71ad8 100644 --- a/target/executable/filter/filter_with_counts/.config.vsh.yaml +++ b/target/executable/filter/filter_with_counts/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_with_counts" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -280,7 +280,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -321,11 +321,11 @@ build_info: output: "target/executable/filter/filter_with_counts" executable: "target/executable/filter/filter_with_counts/filter_with_counts" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -355,7 +355,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/filter_with_counts/filter_with_counts b/target/executable/filter/filter_with_counts/filter_with_counts index 94206ae3..80c37cb5 100755 --- a/target/executable/filter/filter_with_counts/filter_with_counts +++ b/target/executable/filter/filter_with_counts/filter_with_counts @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_with_counts v4.0.1 +# filter_with_counts v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_counts" -LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_with_counts v4.0.1" + echo "filter_with_counts v4.0.2" echo "" echo "Filter scRNA-seq data based on the primary QC metrics." echo "This is based on both the UMI counts, the gene counts" @@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_with_counts v4.0.1" + echo "filter_with_counts v4.0.2" exit ;; --input) @@ -933,7 +933,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_counts:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_counts:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/filter_with_pattern/.config.vsh.yaml b/target/executable/filter/filter_with_pattern/.config.vsh.yaml index 54b18dcf..7162009f 100644 --- a/target/executable/filter/filter_with_pattern/.config.vsh.yaml +++ b/target/executable/filter/filter_with_pattern/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_with_pattern" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -211,7 +211,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -246,11 +246,11 @@ build_info: output: "target/executable/filter/filter_with_pattern" executable: "target/executable/filter/filter_with_pattern/filter_with_pattern" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/filter_with_pattern/filter_with_pattern b/target/executable/filter/filter_with_pattern/filter_with_pattern index 12332387..a7fe4930 100755 --- a/target/executable/filter/filter_with_pattern/filter_with_pattern +++ b/target/executable/filter/filter_with_pattern/filter_with_pattern @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_with_pattern v4.0.1 +# filter_with_pattern v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_pattern" -LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_with_pattern v4.0.1" + echo "filter_with_pattern v4.0.2" echo "" echo "Filter a MuData object based on gene names using a regex." echo "" @@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_with_pattern v4.0.1" + echo "filter_with_pattern v4.0.2" exit ;; --input) @@ -853,7 +853,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_pattern:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_pattern:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/filter_with_scrublet/.config.vsh.yaml b/target/executable/filter/filter_with_scrublet/.config.vsh.yaml index 915e7234..e7ad72b4 100644 --- a/target/executable/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/executable/filter/filter_with_scrublet/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_with_scrublet" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -333,7 +333,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -378,11 +378,11 @@ build_info: output: "target/executable/filter/filter_with_scrublet" executable: "target/executable/filter/filter_with_scrublet/filter_with_scrublet" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -412,7 +412,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/filter_with_scrublet/filter_with_scrublet b/target/executable/filter/filter_with_scrublet/filter_with_scrublet index 6eaf3a99..8aa76008 100755 --- a/target/executable/filter/filter_with_scrublet/filter_with_scrublet +++ b/target/executable/filter/filter_with_scrublet/filter_with_scrublet @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_with_scrublet v4.0.1 +# filter_with_scrublet v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component filter filter_with_scrublet" -LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:16Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm --env NUMBA_CACHE_DIR=/tmp) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_with_scrublet v4.0.1" + echo "filter_with_scrublet v4.0.2" echo "" echo "Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019)." echo "The method tests for potential doublets by using the expression profiles of" @@ -752,7 +752,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_with_scrublet v4.0.1" + echo "filter_with_scrublet v4.0.2" exit ;; --input) @@ -1029,7 +1029,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_scrublet:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/filter_with_scrublet:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/intersect_obs/.config.vsh.yaml b/target/executable/filter/intersect_obs/.config.vsh.yaml index f90fab3c..a63b539e 100644 --- a/target/executable/filter/intersect_obs/.config.vsh.yaml +++ b/target/executable/filter/intersect_obs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "intersect_obs" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -183,7 +183,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -218,11 +218,11 @@ build_info: output: "target/executable/filter/intersect_obs" executable: "target/executable/filter/intersect_obs/intersect_obs" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -252,7 +252,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/intersect_obs/intersect_obs b/target/executable/filter/intersect_obs/intersect_obs index 8dfbd465..38647fb7 100755 --- a/target/executable/filter/intersect_obs/intersect_obs +++ b/target/executable/filter/intersect_obs/intersect_obs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# intersect_obs v4.0.1 +# intersect_obs v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Isabelle Bergiers" LABEL org.opencontainers.image.description="Companion container for running component filter intersect_obs" -LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "intersect_obs v4.0.1" + echo "intersect_obs v4.0.2" echo "" echo "Create an intersection between two or more modalities." echo "" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "intersect_obs v4.0.1" + echo "intersect_obs v4.0.2" exit ;; --input) @@ -796,7 +796,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/intersect_obs:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/intersect_obs:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/remove_modality/.config.vsh.yaml b/target/executable/filter/remove_modality/.config.vsh.yaml index 47b7dcf1..3e67568b 100644 --- a/target/executable/filter/remove_modality/.config.vsh.yaml +++ b/target/executable/filter/remove_modality/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "remove_modality" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -163,7 +163,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,11 @@ build_info: output: "target/executable/filter/remove_modality" executable: "target/executable/filter/remove_modality/remove_modality" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -232,7 +232,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/remove_modality/remove_modality b/target/executable/filter/remove_modality/remove_modality index 0fdb9aa0..1dc2e9f3 100755 --- a/target/executable/filter/remove_modality/remove_modality +++ b/target/executable/filter/remove_modality/remove_modality @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# remove_modality v4.0.1 +# remove_modality v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter remove_modality" -LABEL org.opencontainers.image.created="2026-02-04T09:06:22Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "remove_modality v4.0.1" + echo "remove_modality v4.0.2" echo "" echo "Remove a modality from a .h5mu file" echo "" @@ -651,7 +651,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "remove_modality v4.0.1" + echo "remove_modality v4.0.2" exit ;; --input) @@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/remove_modality:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/remove_modality:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/subset_h5mu/.config.vsh.yaml b/target/executable/filter/subset_h5mu/.config.vsh.yaml index 98135640..5ae9ae18 100644 --- a/target/executable/filter/subset_h5mu/.config.vsh.yaml +++ b/target/executable/filter/subset_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "subset_h5mu" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -177,7 +177,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -212,11 +212,11 @@ build_info: output: "target/executable/filter/subset_h5mu" executable: "target/executable/filter/subset_h5mu/subset_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -246,7 +246,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/subset_h5mu/subset_h5mu b/target/executable/filter/subset_h5mu/subset_h5mu index 28c6ca3c..a7363b47 100755 --- a/target/executable/filter/subset_h5mu/subset_h5mu +++ b/target/executable/filter/subset_h5mu/subset_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# subset_h5mu v4.0.1 +# subset_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component filter subset_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:23Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:17Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "subset_h5mu v4.0.1" + echo "subset_h5mu v4.0.2" echo "" echo "Create a subset of a mudata file by selecting the first number of observations" echo "" @@ -657,7 +657,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "subset_h5mu v4.0.1" + echo "subset_h5mu v4.0.2" exit ;; --input) @@ -803,7 +803,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/filter/subset_obsp/.config.vsh.yaml b/target/executable/filter/subset_obsp/.config.vsh.yaml index a6f9cccc..46173ece 100644 --- a/target/executable/filter/subset_obsp/.config.vsh.yaml +++ b/target/executable/filter/subset_obsp/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "subset_obsp" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -207,7 +207,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -248,11 +248,11 @@ build_info: output: "target/executable/filter/subset_obsp" executable: "target/executable/filter/subset_obsp/subset_obsp" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -282,7 +282,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/filter/subset_obsp/subset_obsp b/target/executable/filter/subset_obsp/subset_obsp index 6f6e14ed..b1ddda29 100755 --- a/target/executable/filter/subset_obsp/subset_obsp +++ b/target/executable/filter/subset_obsp/subset_obsp @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# subset_obsp v4.0.1 +# subset_obsp v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component filter subset_obsp" -LABEL org.opencontainers.image.created="2026-02-04T09:06:21Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:15Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "subset_obsp v4.0.1" + echo "subset_obsp v4.0.2" echo "" echo "Create a subset of an .obsp field in a mudata file, by filtering the columns" echo "based on the values of an .obs column. The resulting subset is moved to an .obsm" @@ -672,7 +672,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "subset_obsp v4.0.1" + echo "subset_obsp v4.0.2" exit ;; --output_compression) @@ -851,7 +851,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_obsp:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/filter/subset_obsp:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/bcftools/.config.vsh.yaml b/target/executable/genetic_demux/bcftools/.config.vsh.yaml index 79544fcb..d0e44c45 100644 --- a/target/executable/genetic_demux/bcftools/.config.vsh.yaml +++ b/target/executable/genetic_demux/bcftools/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcftools" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -195,11 +195,11 @@ build_info: output: "target/executable/genetic_demux/bcftools" executable: "target/executable/genetic_demux/bcftools/bcftools" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -229,7 +229,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/bcftools/bcftools b/target/executable/genetic_demux/bcftools/bcftools index e73dcf1f..62b41c1b 100755 --- a/target/executable/genetic_demux/bcftools/bcftools +++ b/target/executable/genetic_demux/bcftools/bcftools @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bcftools v4.0.1 +# bcftools v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ RUN apt-get update && \ RUN wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2 -O bcftools.tar.bz2 && tar -xjvf bcftools.tar.bz2 && cd bcftools-1.16 && make prefix=/usr/local install LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux bcftools" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bcftools v4.0.1" + echo "bcftools v4.0.2" echo "" echo "Filter the variants called by freebayes or cellSNP" echo "" @@ -650,7 +650,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bcftools v4.0.1" + echo "bcftools v4.0.2" exit ;; --vcf) @@ -790,7 +790,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/bcftools:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/bcftools:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/cellsnp/.config.vsh.yaml b/target/executable/genetic_demux/cellsnp/.config.vsh.yaml index 55a0aa10..1efe94eb 100644 --- a/target/executable/genetic_demux/cellsnp/.config.vsh.yaml +++ b/target/executable/genetic_demux/cellsnp/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellsnp" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -327,7 +327,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -369,11 +369,11 @@ build_info: output: "target/executable/genetic_demux/cellsnp" executable: "target/executable/genetic_demux/cellsnp/cellsnp" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -403,7 +403,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/cellsnp/cellsnp b/target/executable/genetic_demux/cellsnp/cellsnp index 2e57f1ed..5ceca9c2 100755 --- a/target/executable/genetic_demux/cellsnp/cellsnp +++ b/target/executable/genetic_demux/cellsnp/cellsnp @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellsnp v4.0.1 +# cellsnp v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -456,10 +456,10 @@ RUN wget https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.t RUN git clone https://github.com/single-cell-genetics/cellsnp-lite.git && cd cellsnp-lite && autoreconf -iv && ./configure --with-htslib=/htslib-1.16 && make && make install LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux cellsnp" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellsnp v4.0.1" + echo "cellsnp v4.0.2" echo "" echo "cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq" echo "data. It can be directly used for donor deconvolution in multiplexed single-cell" @@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellsnp v4.0.1" + echo "cellsnp v4.0.2" exit ;; --sam_file) @@ -1056,7 +1056,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/cellsnp:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/cellsnp:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/demuxlet/.config.vsh.yaml b/target/executable/genetic_demux/demuxlet/.config.vsh.yaml index d57a893d..3679a4a8 100644 --- a/target/executable/genetic_demux/demuxlet/.config.vsh.yaml +++ b/target/executable/genetic_demux/demuxlet/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "demuxlet" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -455,11 +455,11 @@ build_info: output: "target/executable/genetic_demux/demuxlet" executable: "target/executable/genetic_demux/demuxlet/demuxlet" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -489,7 +489,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/demuxlet/demuxlet b/target/executable/genetic_demux/demuxlet/demuxlet index a7f93cd7..1028df7c 100755 --- a/target/executable/genetic_demux/demuxlet/demuxlet +++ b/target/executable/genetic_demux/demuxlet/demuxlet @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# demuxlet v4.0.1 +# demuxlet v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -460,10 +460,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux demuxlet" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -580,7 +580,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "demuxlet v4.0.1" + echo "demuxlet v4.0.2" echo "" echo "Demuxlet is a software tool to deconvolute sample identity and identify" echo "multiplets when" @@ -782,7 +782,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "demuxlet v4.0.1" + echo "demuxlet v4.0.2" exit ;; --sam) @@ -1187,7 +1187,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/demuxlet:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/demuxlet:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml b/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml index a135f2ba..c68f3836 100644 --- a/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml +++ b/target/executable/genetic_demux/dsc_pileup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "dsc_pileup" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -329,7 +329,7 @@ engines: id: "docker" image: "ubuntu:20.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -367,11 +367,11 @@ build_info: output: "target/executable/genetic_demux/dsc_pileup" executable: "target/executable/genetic_demux/dsc_pileup/dsc_pileup" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -401,7 +401,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/dsc_pileup/dsc_pileup b/target/executable/genetic_demux/dsc_pileup/dsc_pileup index 3993eb6b..8d41169f 100755 --- a/target/executable/genetic_demux/dsc_pileup/dsc_pileup +++ b/target/executable/genetic_demux/dsc_pileup/dsc_pileup @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# dsc_pileup v4.0.1 +# dsc_pileup v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -456,10 +456,10 @@ RUN git clone https://github.com/samtools/htslib.git /tmp/htslib && cd /tmp/htsl RUN git clone --depth 1 https://github.com/statgen/popscle.git /tmp/popscle && mkdir -p /tmp/popscle/build && cd /tmp/popscle/build && cmake .. && make && cp /tmp/popscle/bin/popscle /usr/local/bin LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux dsc_pileup" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "dsc_pileup v4.0.1" + echo "dsc_pileup v4.0.2" echo "" echo "Dsc-pileup is a software tool to pileup reads and corresponding base quality" echo "for each overlapping SNPs and each barcode. By using pileup files," @@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "dsc_pileup v4.0.1" + echo "dsc_pileup v4.0.2" exit ;; --sam) @@ -1058,7 +1058,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/dsc_pileup:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/dsc_pileup:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/freebayes/.config.vsh.yaml b/target/executable/genetic_demux/freebayes/.config.vsh.yaml index 67da6502..613c9e07 100644 --- a/target/executable/genetic_demux/freebayes/.config.vsh.yaml +++ b/target/executable/genetic_demux/freebayes/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "freebayes" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -774,7 +774,7 @@ engines: id: "docker" image: "debian:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -792,11 +792,11 @@ build_info: output: "target/executable/genetic_demux/freebayes" executable: "target/executable/genetic_demux/freebayes/freebayes" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -826,7 +826,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/freebayes/freebayes b/target/executable/genetic_demux/freebayes/freebayes index 925d94fc..170bb069 100755 --- a/target/executable/genetic_demux/freebayes/freebayes +++ b/target/executable/genetic_demux/freebayes/freebayes @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# freebayes v4.0.1 +# freebayes v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux freebayes" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "freebayes v4.0.1" + echo "freebayes v4.0.2" echo "" echo "Freebayes is a Bayesian genetic variant detector designed to" echo "find small polymorphisms, specifically SNPs." @@ -1021,7 +1021,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "freebayes v4.0.1" + echo "freebayes v4.0.2" exit ;; --bam) @@ -1769,7 +1769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freebayes:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freebayes:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml b/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml index fa3dcd2a..0715130c 100644 --- a/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml +++ b/target/executable/genetic_demux/freemuxlet/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "freemuxlet" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -322,7 +322,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -371,11 +371,11 @@ build_info: output: "target/executable/genetic_demux/freemuxlet" executable: "target/executable/genetic_demux/freemuxlet/freemuxlet" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -405,7 +405,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/freemuxlet/freemuxlet b/target/executable/genetic_demux/freemuxlet/freemuxlet index c478957c..3cea95fc 100755 --- a/target/executable/genetic_demux/freemuxlet/freemuxlet +++ b/target/executable/genetic_demux/freemuxlet/freemuxlet @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# freemuxlet v4.0.1 +# freemuxlet v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -460,10 +460,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux freemuxlet" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -580,7 +580,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "freemuxlet v4.0.1" + echo "freemuxlet v4.0.2" echo "" echo "Freemuxlet is a software tool to deconvolute sample identity and identify" echo "multiplets when" @@ -742,7 +742,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "freemuxlet v4.0.1" + echo "freemuxlet v4.0.2" exit ;; --plp) @@ -1052,7 +1052,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freemuxlet:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/freemuxlet:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/samtools/.config.vsh.yaml b/target/executable/genetic_demux/samtools/.config.vsh.yaml index 9eb1979f..34900d02 100644 --- a/target/executable/genetic_demux/samtools/.config.vsh.yaml +++ b/target/executable/genetic_demux/samtools/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -138,7 +138,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -173,11 +173,11 @@ build_info: output: "target/executable/genetic_demux/samtools" executable: "target/executable/genetic_demux/samtools/samtools" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -207,7 +207,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/samtools/samtools b/target/executable/genetic_demux/samtools/samtools index 9c641238..134e4689 100755 --- a/target/executable/genetic_demux/samtools/samtools +++ b/target/executable/genetic_demux/samtools/samtools @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools v4.0.1 +# samtools v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux samtools" -LABEL org.opencontainers.image.created="2026-02-04T09:06:10Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools v4.0.1" + echo "samtools v4.0.2" echo "" echo "Filter the BAM according to the instruction of scSplit via Samtools." echo "" @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools v4.0.1" + echo "samtools v4.0.2" exit ;; --bam) @@ -752,7 +752,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/samtools:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/samtools:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/scsplit/.config.vsh.yaml b/target/executable/genetic_demux/scsplit/.config.vsh.yaml index bd75ed0a..9a102cc8 100644 --- a/target/executable/genetic_demux/scsplit/.config.vsh.yaml +++ b/target/executable/genetic_demux/scsplit/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scsplit" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -265,7 +265,7 @@ engines: id: "docker" image: "python:3.13" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -301,11 +301,11 @@ build_info: output: "target/executable/genetic_demux/scsplit" executable: "target/executable/genetic_demux/scsplit/scsplit" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -335,7 +335,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/scsplit/scsplit b/target/executable/genetic_demux/scsplit/scsplit index d54144f2..7a13fdd9 100755 --- a/target/executable/genetic_demux/scsplit/scsplit +++ b/target/executable/genetic_demux/scsplit/scsplit @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scsplit v4.0.1 +# scsplit v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ RUN git clone https://github.com/jon-xu/scSplit && cd scSplit && git apply /opt/scSplit.patch && cp scSplit /usr/local/bin && cd .. && rm -rf scSplit LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux scsplit" -LABEL org.opencontainers.image.created="2026-02-04T09:06:07Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:02Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scsplit v4.0.1" + echo "scsplit v4.0.2" echo "" echo "scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq," echo "using a hidden state model for identifying genetically distinct samples within a" @@ -702,7 +702,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scsplit v4.0.1" + echo "scsplit v4.0.2" exit ;; --vcf) @@ -958,7 +958,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/scsplit:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/scsplit:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/souporcell/.config.vsh.yaml b/target/executable/genetic_demux/souporcell/.config.vsh.yaml index e2e44fbc..821dcb5e 100644 --- a/target/executable/genetic_demux/souporcell/.config.vsh.yaml +++ b/target/executable/genetic_demux/souporcell/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "souporcell" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -272,7 +272,7 @@ engines: id: "docker" image: "cumulusprod/souporcell:2022.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -285,11 +285,11 @@ build_info: output: "target/executable/genetic_demux/souporcell" executable: "target/executable/genetic_demux/souporcell/souporcell" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -319,7 +319,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/souporcell/souporcell b/target/executable/genetic_demux/souporcell/souporcell index d3aa0952..fa41e0fd 100755 --- a/target/executable/genetic_demux/souporcell/souporcell +++ b/target/executable/genetic_demux/souporcell/souporcell @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# souporcell v4.0.1 +# souporcell v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ FROM cumulusprod/souporcell:2022.12 ENTRYPOINT [] LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux souporcell" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "souporcell v4.0.1" + echo "souporcell v4.0.2" echo "" echo "souporcell is a method for clustering mixed-genotype scRNAseq experiments by" echo "individual." @@ -698,7 +698,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "souporcell v4.0.1" + echo "souporcell v4.0.2" exit ;; --fasta) @@ -959,7 +959,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/souporcell:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/souporcell:v4.0.2' fi # print dockerfile diff --git a/target/executable/genetic_demux/vireo/.config.vsh.yaml b/target/executable/genetic_demux/vireo/.config.vsh.yaml index 1707f6b8..9e4cabc3 100644 --- a/target/executable/genetic_demux/vireo/.config.vsh.yaml +++ b/target/executable/genetic_demux/vireo/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "vireo" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -285,7 +285,7 @@ engines: id: "docker" image: "python:3.13" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -305,11 +305,11 @@ build_info: output: "target/executable/genetic_demux/vireo" executable: "target/executable/genetic_demux/vireo/vireo" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -339,7 +339,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/genetic_demux/vireo/vireo b/target/executable/genetic_demux/vireo/vireo index e779495d..a516e976 100755 --- a/target/executable/genetic_demux/vireo/vireo +++ b/target/executable/genetic_demux/vireo/vireo @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# vireo v4.0.1 +# vireo v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Xichen Wu" LABEL org.opencontainers.image.description="Companion container for running component genetic_demux vireo" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:02Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "vireo v4.0.1" + echo "vireo v4.0.2" echo "" echo "Vireo is primarily designed for demultiplexing cells into donors by modelling of" echo "expressed alleles." @@ -706,7 +706,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "vireo v4.0.1" + echo "vireo v4.0.2" exit ;; --cell_data) @@ -979,7 +979,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/vireo:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/genetic_demux/vireo:v4.0.2' fi # print dockerfile diff --git a/target/executable/integrate/harmonypy/.config.vsh.yaml b/target/executable/integrate/harmonypy/.config.vsh.yaml index 77e4b4b8..d7930215 100644 --- a/target/executable/integrate/harmonypy/.config.vsh.yaml +++ b/target/executable/integrate/harmonypy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "harmonypy" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -232,7 +232,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -275,11 +275,11 @@ build_info: output: "target/executable/integrate/harmonypy" executable: "target/executable/integrate/harmonypy/harmonypy" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -309,7 +309,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/integrate/harmonypy/harmonypy b/target/executable/integrate/harmonypy/harmonypy index 94fc318b..9292f141 100755 --- a/target/executable/integrate/harmonypy/harmonypy +++ b/target/executable/integrate/harmonypy/harmonypy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# harmonypy v4.0.1 +# harmonypy v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component integrate harmonypy" -LABEL org.opencontainers.image.created="2026-02-04T09:06:29Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:23Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "harmonypy v4.0.1" + echo "harmonypy v4.0.2" echo "" echo "Performs Harmony integration based as described in" echo "https://github.com/immunogenomics/harmony. Based on an implementation in python" @@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "harmonypy v4.0.1" + echo "harmonypy v4.0.2" exit ;; --input) @@ -879,7 +879,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/harmonypy:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/harmonypy:v4.0.2' fi # print dockerfile diff --git a/target/executable/integrate/scanorama/.config.vsh.yaml b/target/executable/integrate/scanorama/.config.vsh.yaml index 61286ec0..9d578e7f 100644 --- a/target/executable/integrate/scanorama/.config.vsh.yaml +++ b/target/executable/integrate/scanorama/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanorama" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -269,7 +269,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -313,11 +313,11 @@ build_info: output: "target/executable/integrate/scanorama" executable: "target/executable/integrate/scanorama/scanorama" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -347,7 +347,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/integrate/scanorama/scanorama b/target/executable/integrate/scanorama/scanorama index 0328014b..ea9afc5a 100755 --- a/target/executable/integrate/scanorama/scanorama +++ b/target/executable/integrate/scanorama/scanorama @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scanorama v4.0.1 +# scanorama v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integrate scanorama" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:02Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scanorama v4.0.1" + echo "scanorama v4.0.2" echo "" echo "Use Scanorama to integrate different experiments." echo "" @@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scanorama v4.0.1" + echo "scanorama v4.0.2" exit ;; --input) @@ -931,7 +931,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scanorama:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scanorama:v4.0.2' fi # print dockerfile diff --git a/target/executable/integrate/scarches/.config.vsh.yaml b/target/executable/integrate/scarches/.config.vsh.yaml index f3c9a512..e2212dd6 100644 --- a/target/executable/integrate/scarches/.config.vsh.yaml +++ b/target/executable/integrate/scarches/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scarches" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -442,7 +442,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -474,11 +474,11 @@ build_info: output: "target/executable/integrate/scarches" executable: "target/executable/integrate/scarches/scarches" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -508,7 +508,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/integrate/scarches/scarches b/target/executable/integrate/scarches/scarches index 1e5dd1da..a905fd23 100755 --- a/target/executable/integrate/scarches/scarches +++ b/target/executable/integrate/scarches/scarches @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scarches v4.0.1 +# scarches v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component integrate scarches" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scarches v4.0.1" + echo "scarches v4.0.2" echo "" echo "Performs reference mapping with scArches" echo "" @@ -789,7 +789,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scarches v4.0.1" + echo "scarches v4.0.2" exit ;; --input) @@ -1196,7 +1196,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scarches:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scarches:v4.0.2' fi # print dockerfile diff --git a/target/executable/integrate/scvi/.config.vsh.yaml b/target/executable/integrate/scvi/.config.vsh.yaml index 3ad5c0f1..c3192c35 100644 --- a/target/executable/integrate/scvi/.config.vsh.yaml +++ b/target/executable/integrate/scvi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvi" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Malte D. Luecken" roles: @@ -563,7 +563,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -600,11 +600,11 @@ build_info: output: "target/executable/integrate/scvi" executable: "target/executable/integrate/scvi/scvi" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -634,7 +634,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/integrate/scvi/scvi b/target/executable/integrate/scvi/scvi index e976e1cf..cdf85bf9 100755 --- a/target/executable/integrate/scvi/scvi +++ b/target/executable/integrate/scvi/scvi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scvi v4.0.1 +# scvi v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Malte D. Luecken, Dries Schaumont, Matthias Beyens" LABEL org.opencontainers.image.description="Companion container for running component integrate scvi" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:02Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scvi v4.0.1" + echo "scvi v4.0.2" echo "" echo "Performs scvi integration as done in the human lung cell atlas" echo "https://github.com/LungCellAtlas/HLCA" @@ -856,7 +856,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scvi v4.0.1" + echo "scvi v4.0.2" exit ;; --input) @@ -1349,7 +1349,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scvi:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/scvi:v4.0.2' fi # print dockerfile diff --git a/target/executable/integrate/totalvi/.config.vsh.yaml b/target/executable/integrate/totalvi/.config.vsh.yaml index a3dc336c..39233198 100644 --- a/target/executable/integrate/totalvi/.config.vsh.yaml +++ b/target/executable/integrate/totalvi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -484,7 +484,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -517,11 +517,11 @@ build_info: output: "target/executable/integrate/totalvi" executable: "target/executable/integrate/totalvi/totalvi" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -551,7 +551,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/integrate/totalvi/totalvi b/target/executable/integrate/totalvi/totalvi index e3ac42b8..92a6fc5f 100755 --- a/target/executable/integrate/totalvi/totalvi +++ b/target/executable/integrate/totalvi/totalvi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# totalvi v4.0.1 +# totalvi v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component integrate totalvi" -LABEL org.opencontainers.image.created="2026-02-04T09:06:08Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "totalvi v4.0.1" + echo "totalvi v4.0.2" echo "" echo "Performs TotalVI integration of CITE-seq and scRNA-seq data." echo "" @@ -824,7 +824,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "totalvi v4.0.1" + echo "totalvi v4.0.2" exit ;; --input) @@ -1263,7 +1263,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi:v4.0.2' fi # print dockerfile diff --git a/target/executable/integrate/totalvi_scarches/.config.vsh.yaml b/target/executable/integrate/totalvi_scarches/.config.vsh.yaml index 84b0af30..b1c2a3f3 100644 --- a/target/executable/integrate/totalvi_scarches/.config.vsh.yaml +++ b/target/executable/integrate/totalvi_scarches/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi_scarches" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" info: @@ -353,7 +353,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -385,11 +385,11 @@ build_info: output: "target/executable/integrate/totalvi_scarches" executable: "target/executable/integrate/totalvi_scarches/totalvi_scarches" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -419,7 +419,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/integrate/totalvi_scarches/totalvi_scarches b/target/executable/integrate/totalvi_scarches/totalvi_scarches index f18c0c91..a1755a75 100755 --- a/target/executable/integrate/totalvi_scarches/totalvi_scarches +++ b/target/executable/integrate/totalvi_scarches/totalvi_scarches @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# totalvi_scarches v4.0.1 +# totalvi_scarches v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component integrate totalvi_scarches" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:03Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "totalvi_scarches v4.0.1" + echo "totalvi_scarches v4.0.2" echo "" echo "Performs totalVI integration by mapping the query dataset to a reference dataset" echo "or model." @@ -745,7 +745,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "totalvi_scarches v4.0.1" + echo "totalvi_scarches v4.0.2" exit ;; --input) @@ -1107,7 +1107,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi_scarches:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/integrate/totalvi_scarches:v4.0.2' fi # print dockerfile diff --git a/target/executable/interpret/lianapy/.config.vsh.yaml b/target/executable/interpret/lianapy/.config.vsh.yaml index d97c2c9b..c2bd4c6a 100644 --- a/target/executable/interpret/lianapy/.config.vsh.yaml +++ b/target/executable/interpret/lianapy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lianapy" namespace: "interpret" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Mauro Saporita" roles: @@ -320,7 +320,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -357,11 +357,11 @@ build_info: output: "target/executable/interpret/lianapy" executable: "target/executable/interpret/lianapy/lianapy" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -391,7 +391,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/interpret/lianapy/lianapy b/target/executable/interpret/lianapy/lianapy index 536ec3f4..31ca9186 100755 --- a/target/executable/interpret/lianapy/lianapy +++ b/target/executable/interpret/lianapy/lianapy @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# lianapy v4.0.1 +# lianapy v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Mauro Saporita, Povilas Gibas" LABEL org.opencontainers.image.description="Companion container for running component interpret lianapy" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "lianapy v4.0.1" + echo "lianapy v4.0.2" echo "" echo "Performs LIANA integration based as described in" echo "https://github.com/saezlab/liana-py" @@ -722,7 +722,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "lianapy v4.0.1" + echo "lianapy v4.0.2" exit ;; --input) @@ -996,7 +996,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/interpret/lianapy:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/interpret/lianapy:v4.0.2' fi # print dockerfile diff --git a/target/executable/labels_transfer/knn/.config.vsh.yaml b/target/executable/labels_transfer/knn/.config.vsh.yaml index 00d6dee5..250eaf3d 100644 --- a/target/executable/labels_transfer/knn/.config.vsh.yaml +++ b/target/executable/labels_transfer/knn/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "knn" namespace: "labels_transfer" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -455,11 +455,11 @@ build_info: output: "target/executable/labels_transfer/knn" executable: "target/executable/labels_transfer/knn/knn" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -489,7 +489,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/labels_transfer/knn/knn b/target/executable/labels_transfer/knn/knn index 425d5678..86921a30 100755 --- a/target/executable/labels_transfer/knn/knn +++ b/target/executable/labels_transfer/knn/knn @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# knn v4.0.1 +# knn v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -462,10 +462,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component labels_transfer knn" -LABEL org.opencontainers.image.created="2026-02-04T09:06:20Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:15Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -582,7 +582,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "knn v4.0.1" + echo "knn v4.0.2" echo "" echo "This component performs label transfer from reference to query using a K-Neirest" echo "Neighbors classifier." @@ -738,7 +738,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "knn v4.0.1" + echo "knn v4.0.2" exit ;; --input) @@ -1001,7 +1001,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/knn:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/knn:v4.0.2' fi # print dockerfile diff --git a/target/executable/labels_transfer/xgboost/.config.vsh.yaml b/target/executable/labels_transfer/xgboost/.config.vsh.yaml index 0d14e4f7..57701fdb 100644 --- a/target/executable/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/executable/labels_transfer/xgboost/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "xgboost" namespace: "labels_transfer" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -555,7 +555,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -604,11 +604,11 @@ build_info: output: "target/executable/labels_transfer/xgboost" executable: "target/executable/labels_transfer/xgboost/xgboost" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -638,7 +638,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/labels_transfer/xgboost/xgboost b/target/executable/labels_transfer/xgboost/xgboost index 83390858..9721ca94 100755 --- a/target/executable/labels_transfer/xgboost/xgboost +++ b/target/executable/labels_transfer/xgboost/xgboost @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# xgboost v4.0.1 +# xgboost v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -465,10 +465,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component labels_transfer xgboost" -LABEL org.opencontainers.image.created="2026-02-04T09:06:20Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:14Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "xgboost v4.0.1" + echo "xgboost v4.0.2" echo "" echo "Performs label transfer from reference to query using XGBoost classifier" echo "" @@ -839,7 +839,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "xgboost v4.0.1" + echo "xgboost v4.0.2" exit ;; --input) @@ -1291,7 +1291,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/xgboost:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/labels_transfer/xgboost:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/bd_rhapsody/.config.vsh.yaml b/target/executable/mapping/bd_rhapsody/.config.vsh.yaml index fe2afc14..1af56de2 100644 --- a/target/executable/mapping/bd_rhapsody/.config.vsh.yaml +++ b/target/executable/mapping/bd_rhapsody/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -1098,7 +1098,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -1125,11 +1125,11 @@ build_info: output: "target/executable/mapping/bd_rhapsody" executable: "target/executable/mapping/bd_rhapsody/bd_rhapsody" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -1159,7 +1159,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/bd_rhapsody/bd_rhapsody b/target/executable/mapping/bd_rhapsody/bd_rhapsody index 772e16fe..4d25ca9e 100755 --- a/target/executable/mapping/bd_rhapsody/bd_rhapsody +++ b/target/executable/mapping/bd_rhapsody/bd_rhapsody @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bd_rhapsody v4.0.1 +# bd_rhapsody v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component mapping bd_rhapsody" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bd_rhapsody v4.0.1" + echo "bd_rhapsody v4.0.2" echo "" echo "BD Rhapsody Sequence Analysis CWL pipeline v2.2.1" echo "This pipeline performs analysis of single-cell multiomic sequence read (FASTQ)" @@ -1113,7 +1113,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bd_rhapsody v4.0.1" + echo "bd_rhapsody v4.0.2" exit ;; --reads) @@ -1964,7 +1964,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/bd_rhapsody:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/bd_rhapsody:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml b/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml index 49e3f2a5..2a4e4526 100644 --- a/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml +++ b/target/executable/mapping/cellranger_atac_count/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_atac_count" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -235,7 +235,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger_atac:2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -253,11 +253,11 @@ build_info: output: "target/executable/mapping/cellranger_atac_count" executable: "target/executable/mapping/cellranger_atac_count/cellranger_atac_count" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -287,7 +287,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/cellranger_atac_count/cellranger_atac_count b/target/executable/mapping/cellranger_atac_count/cellranger_atac_count index 14e5ae92..e3e2b05f 100755 --- a/target/executable/mapping/cellranger_atac_count/cellranger_atac_count +++ b/target/executable/mapping/cellranger_atac_count/cellranger_atac_count @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_atac_count v4.0.1 +# cellranger_atac_count v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ RUN DEBIAN_FRONTEND=noninteractive apt update \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_atac_count" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_atac_count v4.0.1" + echo "cellranger_atac_count v4.0.2" echo "" echo "Align fastq files using Cell Ranger ATAC count." echo "" @@ -681,7 +681,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_atac_count v4.0.1" + echo "cellranger_atac_count v4.0.2" exit ;; --input) @@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_atac_count:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_atac_count:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/cellranger_count/.config.vsh.yaml b/target/executable/mapping/cellranger_count/.config.vsh.yaml index c46f6ab3..6910556d 100644 --- a/target/executable/mapping/cellranger_count/.config.vsh.yaml +++ b/target/executable/mapping/cellranger_count/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_count" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -367,7 +367,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -397,11 +397,11 @@ build_info: output: "target/executable/mapping/cellranger_count" executable: "target/executable/mapping/cellranger_count/cellranger_count" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -431,7 +431,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/cellranger_count/cellranger_count b/target/executable/mapping/cellranger_count/cellranger_count index b2b7c3e4..03a250fb 100755 --- a/target/executable/mapping/cellranger_count/cellranger_count +++ b/target/executable/mapping/cellranger_count/cellranger_count @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_count v4.0.1 +# cellranger_count v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_count v4.0.1" + echo "cellranger_count v4.0.2" echo "" echo "Align fastq files using Cell Ranger count." echo "" @@ -747,7 +747,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_count v4.0.1" + echo "cellranger_count v4.0.2" exit ;; --input) @@ -1037,7 +1037,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/cellranger_count_split/.config.vsh.yaml b/target/executable/mapping/cellranger_count_split/.config.vsh.yaml index a78ad9cd..4863809b 100644 --- a/target/executable/mapping/cellranger_count_split/.config.vsh.yaml +++ b/target/executable/mapping/cellranger_count_split/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_count_split" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "ubuntu:jammy" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -241,11 +241,11 @@ build_info: output: "target/executable/mapping/cellranger_count_split" executable: "target/executable/mapping/cellranger_count_split/cellranger_count_split" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -275,7 +275,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/cellranger_count_split/cellranger_count_split b/target/executable/mapping/cellranger_count_split/cellranger_count_split index e77bc8b5..375e15f7 100755 --- a/target/executable/mapping/cellranger_count_split/cellranger_count_split +++ b/target/executable/mapping/cellranger_count_split/cellranger_count_split @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_count_split v4.0.1 +# cellranger_count_split v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ ENTRYPOINT [] RUN apt update && apt upgrade -y LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Samuel D'Souza, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_count_split" -LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_count_split v4.0.1" + echo "cellranger_count_split v4.0.2" echo "" echo "Split 10x Cell Ranger output directory into separate output fields." echo "" @@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_count_split v4.0.1" + echo "cellranger_count_split v4.0.2" exit ;; --input) @@ -828,7 +828,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count_split:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_count_split:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/cellranger_multi/.config.vsh.yaml b/target/executable/mapping/cellranger_multi/.config.vsh.yaml index b20af07d..16196804 100644 --- a/target/executable/mapping/cellranger_multi/.config.vsh.yaml +++ b/target/executable/mapping/cellranger_multi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_multi" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -952,7 +952,7 @@ engines: id: "docker" image: "quay.io/nf-core/cellranger:10.0.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -991,11 +991,11 @@ build_info: output: "target/executable/mapping/cellranger_multi" executable: "target/executable/mapping/cellranger_multi/cellranger_multi" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -1025,7 +1025,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/cellranger_multi/cellranger_multi b/target/executable/mapping/cellranger_multi/cellranger_multi index ddb2852a..268c3b51 100755 --- a/target/executable/mapping/cellranger_multi/cellranger_multi +++ b/target/executable/mapping/cellranger_multi/cellranger_multi @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_multi v4.0.1 +# cellranger_multi v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -463,10 +463,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer, Weiwei Schultz, Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component mapping cellranger_multi" -LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -583,7 +583,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_multi v4.0.1" + echo "cellranger_multi v4.0.2" echo "" echo "Align fastq files using Cell Ranger multi." echo "" @@ -1133,7 +1133,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_multi v4.0.1" + echo "cellranger_multi v4.0.2" exit ;; --input) @@ -1983,7 +1983,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_multi:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/cellranger_multi:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/htseq_count/.config.vsh.yaml b/target/executable/mapping/htseq_count/.config.vsh.yaml index 376c671e..9f70d08d 100644 --- a/target/executable/mapping/htseq_count/.config.vsh.yaml +++ b/target/executable/mapping/htseq_count/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htseq_count" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -396,7 +396,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -422,11 +422,11 @@ build_info: output: "target/executable/mapping/htseq_count" executable: "target/executable/mapping/htseq_count/htseq_count" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -456,7 +456,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/htseq_count/htseq_count b/target/executable/mapping/htseq_count/htseq_count index 4c15cc45..b2e1933a 100755 --- a/target/executable/mapping/htseq_count/htseq_count +++ b/target/executable/mapping/htseq_count/htseq_count @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# htseq_count v4.0.1 +# htseq_count v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "htseq_count v4.0.1" + echo "htseq_count v4.0.2" echo "" echo "Quantify gene expression for subsequent testing for differential expression." echo "" @@ -762,7 +762,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "htseq_count v4.0.1" + echo "htseq_count v4.0.2" exit ;; --input) @@ -1102,7 +1102,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml index e07c182a..f0af8648 100644 --- a/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml +++ b/target/executable/mapping/htseq_count_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htseq_count_to_h5mu" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -201,7 +201,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -236,11 +236,11 @@ build_info: output: "target/executable/mapping/htseq_count_to_h5mu" executable: "target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -270,7 +270,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu b/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu index d994bbd6..5fe2b614 100755 --- a/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu +++ b/target/executable/mapping/htseq_count_to_h5mu/htseq_count_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# htseq_count_to_h5mu v4.0.1 +# htseq_count_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -462,10 +462,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping htseq_count_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -582,7 +582,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "htseq_count_to_h5mu v4.0.1" + echo "htseq_count_to_h5mu v4.0.2" echo "" echo "Convert the htseq table to a h5mu." echo "" @@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "htseq_count_to_h5mu v4.0.1" + echo "htseq_count_to_h5mu v4.0.2" exit ;; --input_id) @@ -826,7 +826,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/htseq_count_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/multi_star/.config.vsh.yaml b/target/executable/mapping/multi_star/.config.vsh.yaml index 32f30019..93ded6f3 100644 --- a/target/executable/mapping/multi_star/.config.vsh.yaml +++ b/target/executable/mapping/multi_star/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "multi_star" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2856,7 +2856,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -2904,11 +2904,11 @@ build_info: output: "target/executable/mapping/multi_star" executable: "target/executable/mapping/multi_star/multi_star" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -2938,7 +2938,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/multi_star/multi_star b/target/executable/mapping/multi_star/multi_star index 1a6c382e..1632ed11 100755 --- a/target/executable/mapping/multi_star/multi_star +++ b/target/executable/mapping/multi_star/multi_star @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multi_star v4.0.1 +# multi_star v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -473,10 +473,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star" -LABEL org.opencontainers.image.created="2026-02-04T09:06:11Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -593,7 +593,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multi_star v4.0.1" + echo "multi_star v4.0.2" echo "" echo "Align fastq files using STAR." echo "" @@ -2097,7 +2097,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multi_star v4.0.1" + echo "multi_star v4.0.2" exit ;; --input_id) @@ -4637,7 +4637,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml index f83caec6..fb90002e 100644 --- a/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml +++ b/target/executable/mapping/multi_star_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "multi_star_to_h5mu" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -177,7 +177,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -206,11 +206,11 @@ build_info: output: "target/executable/mapping/multi_star_to_h5mu" executable: "target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -240,7 +240,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu b/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu index af8bcdea..61ecd050 100755 --- a/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu +++ b/target/executable/mapping/multi_star_to_h5mu/multi_star_to_h5mu @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multi_star_to_h5mu v4.0.1 +# multi_star_to_h5mu v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping multi_star_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multi_star_to_h5mu v4.0.1" + echo "multi_star_to_h5mu v4.0.2" echo "" echo "Convert the output of \`multi_star\` to a h5mu." echo "" @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multi_star_to_h5mu v4.0.1" + echo "multi_star_to_h5mu v4.0.2" exit ;; --input) @@ -778,7 +778,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star_to_h5mu:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/multi_star_to_h5mu:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/samtools_sort/.config.vsh.yaml b/target/executable/mapping/samtools_sort/.config.vsh.yaml index 0b8a13b0..70b5bfa2 100644 --- a/target/executable/mapping/samtools_sort/.config.vsh.yaml +++ b/target/executable/mapping/samtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_sort" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -258,7 +258,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -282,11 +282,11 @@ build_info: output: "target/executable/mapping/samtools_sort" executable: "target/executable/mapping/samtools_sort/samtools_sort" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -316,7 +316,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/samtools_sort/samtools_sort b/target/executable/mapping/samtools_sort/samtools_sort index c22d69cf..7511415e 100755 --- a/target/executable/mapping/samtools_sort/samtools_sort +++ b/target/executable/mapping/samtools_sort/samtools_sort @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# samtools_sort v4.0.1 +# samtools_sort v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Angela Oliveira Pisco" LABEL org.opencontainers.image.description="Companion container for running component mapping samtools_sort" -LABEL org.opencontainers.image.created="2026-02-04T09:06:14Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:09Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "samtools_sort v4.0.1" + echo "samtools_sort v4.0.2" echo "" echo "Sort and (optionally) index alignments." echo "" @@ -702,7 +702,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "samtools_sort v4.0.1" + echo "samtools_sort v4.0.2" exit ;; --input) @@ -885,7 +885,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/samtools_sort:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/samtools_sort:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/star_align/.config.vsh.yaml b/target/executable/mapping/star_align/.config.vsh.yaml index cb90395a..6d00d9fe 100644 --- a/target/executable/mapping/star_align/.config.vsh.yaml +++ b/target/executable/mapping/star_align/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2341,7 +2341,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -2371,11 +2371,11 @@ build_info: output: "target/executable/mapping/star_align" executable: "target/executable/mapping/star_align/star_align" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -2405,7 +2405,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/star_align/star_align b/target/executable/mapping/star_align/star_align index 65d632fc..8e86dc38 100755 --- a/target/executable/mapping/star_align/star_align +++ b/target/executable/mapping/star_align/star_align @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_align v4.0.1 +# star_align v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -470,10 +470,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping star_align" -LABEL org.opencontainers.image.created="2026-02-04T09:06:13Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -590,7 +590,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_align v4.0.1" + echo "star_align v4.0.2" echo "" echo "Align fastq files using STAR." echo "" @@ -2025,7 +2025,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_align v4.0.1" + echo "star_align v4.0.2" exit ;; --input) @@ -4415,7 +4415,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align:v4.0.2' fi # print dockerfile diff --git a/target/executable/mapping/star_align_v273a/.config.vsh.yaml b/target/executable/mapping/star_align_v273a/.config.vsh.yaml index e1528c89..d1f81d78 100644 --- a/target/executable/mapping/star_align_v273a/.config.vsh.yaml +++ b/target/executable/mapping/star_align_v273a/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align_v273a" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2341,7 +2341,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -2371,11 +2371,11 @@ build_info: output: "target/executable/mapping/star_align_v273a" executable: "target/executable/mapping/star_align_v273a/star_align_v273a" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -2405,7 +2405,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/mapping/star_align_v273a/star_align_v273a b/target/executable/mapping/star_align_v273a/star_align_v273a index e85782b7..ea9a6461 100755 --- a/target/executable/mapping/star_align_v273a/star_align_v273a +++ b/target/executable/mapping/star_align_v273a/star_align_v273a @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# star_align_v273a v4.0.1 +# star_align_v273a v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -470,10 +470,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component mapping star_align_v273a" -LABEL org.opencontainers.image.created="2026-02-04T09:06:12Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -590,7 +590,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "star_align_v273a v4.0.1" + echo "star_align_v273a v4.0.2" echo "" echo "Align fastq files using STAR." echo "" @@ -2025,7 +2025,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "star_align_v273a v4.0.1" + echo "star_align_v273a v4.0.2" exit ;; --input) @@ -4415,7 +4415,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align_v273a:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/mapping/star_align_v273a:v4.0.2' fi # print dockerfile diff --git a/target/executable/metadata/add_id/.config.vsh.yaml b/target/executable/metadata/add_id/.config.vsh.yaml index 0f9a97d5..59b748bd 100644 --- a/target/executable/metadata/add_id/.config.vsh.yaml +++ b/target/executable/metadata/add_id/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "add_id" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -185,7 +185,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -226,11 +226,11 @@ build_info: output: "target/executable/metadata/add_id" executable: "target/executable/metadata/add_id/add_id" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -260,7 +260,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/metadata/add_id/add_id b/target/executable/metadata/add_id/add_id index 5bbd7d36..e7131c12 100755 --- a/target/executable/metadata/add_id/add_id +++ b/target/executable/metadata/add_id/add_id @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# add_id v4.0.1 +# add_id v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata add_id" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "add_id v4.0.1" + echo "add_id v4.0.2" echo "" echo "Add id of .obs. Also allows to make .obs_names (the .obs index) unique" echo "by prefixing the values with an unique id per .h5mu file." @@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "add_id v4.0.1" + echo "add_id v4.0.2" exit ;; --input) @@ -824,7 +824,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/add_id:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/add_id:v4.0.2' fi # print dockerfile diff --git a/target/executable/metadata/grep_annotation_column/.config.vsh.yaml b/target/executable/metadata/grep_annotation_column/.config.vsh.yaml index 5127ae71..2c61583a 100644 --- a/target/executable/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/executable/metadata/grep_annotation_column/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "grep_annotation_column" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -241,7 +241,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -282,11 +282,11 @@ build_info: output: "target/executable/metadata/grep_annotation_column" executable: "target/executable/metadata/grep_annotation_column/grep_annotation_column" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -316,7 +316,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/metadata/grep_annotation_column/grep_annotation_column b/target/executable/metadata/grep_annotation_column/grep_annotation_column index e8fa0959..57804a2d 100755 --- a/target/executable/metadata/grep_annotation_column/grep_annotation_column +++ b/target/executable/metadata/grep_annotation_column/grep_annotation_column @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# grep_annotation_column v4.0.1 +# grep_annotation_column v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata grep_annotation_column" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "grep_annotation_column v4.0.1" + echo "grep_annotation_column v4.0.2" echo "" echo "Perform a regex lookup on a column from the annotation matrices .obs or .var." echo "The annotation matrix can originate from either a modality, or all modalities" @@ -694,7 +694,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "grep_annotation_column v4.0.1" + echo "grep_annotation_column v4.0.2" exit ;; --input) @@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/grep_annotation_column:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/grep_annotation_column:v4.0.2' fi # print dockerfile diff --git a/target/executable/metadata/join_csv/.config.vsh.yaml b/target/executable/metadata/join_csv/.config.vsh.yaml index 32e01732..79f59a40 100644 --- a/target/executable/metadata/join_csv/.config.vsh.yaml +++ b/target/executable/metadata/join_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "join_csv" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -216,7 +216,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -257,11 +257,11 @@ build_info: output: "target/executable/metadata/join_csv" executable: "target/executable/metadata/join_csv/join_csv" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -291,7 +291,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/metadata/join_csv/join_csv b/target/executable/metadata/join_csv/join_csv index 8e3e457d..40caa692 100755 --- a/target/executable/metadata/join_csv/join_csv +++ b/target/executable/metadata/join_csv/join_csv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# join_csv v4.0.1 +# join_csv v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata join_csv" -LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "join_csv v4.0.1" + echo "join_csv v4.0.2" echo "" echo "Join a csv containing metadata to the .obs or .var field of a mudata file." echo "" @@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "join_csv v4.0.1" + echo "join_csv v4.0.2" exit ;; --input) @@ -867,7 +867,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_csv:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_csv:v4.0.2' fi # print dockerfile diff --git a/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml b/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml index ad948f7e..3f07aa1a 100644 --- a/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml +++ b/target/executable/metadata/join_uns_to_obs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "join_uns_to_obs" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -164,7 +164,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -205,11 +205,11 @@ build_info: output: "target/executable/metadata/join_uns_to_obs" executable: "target/executable/metadata/join_uns_to_obs/join_uns_to_obs" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -239,7 +239,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/metadata/join_uns_to_obs/join_uns_to_obs b/target/executable/metadata/join_uns_to_obs/join_uns_to_obs index 1c31c939..0d683e79 100755 --- a/target/executable/metadata/join_uns_to_obs/join_uns_to_obs +++ b/target/executable/metadata/join_uns_to_obs/join_uns_to_obs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# join_uns_to_obs v4.0.1 +# join_uns_to_obs v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ python -c 'exec("try:\n import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n exit(0)\nelse: assert int(version(\"zarr\").partition(\".\")[0]) > 2")' LABEL org.opencontainers.image.description="Companion container for running component metadata join_uns_to_obs" -LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "join_uns_to_obs v4.0.1" + echo "join_uns_to_obs v4.0.2" echo "" echo "Join a data frame of length 1 (1 row index value) in .uns containing metadata to" echo "the .obs of a mudata file." @@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "join_uns_to_obs v4.0.1" + echo "join_uns_to_obs v4.0.2" exit ;; --input) @@ -810,7 +810,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_uns_to_obs:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/join_uns_to_obs:v4.0.2' fi # print dockerfile diff --git a/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml index 18047ed1..30d50ac5 100644 --- a/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/executable/metadata/move_obsm_to_obs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_obsm_to_obs" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -183,7 +183,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -224,11 +224,11 @@ build_info: output: "target/executable/metadata/move_obsm_to_obs" executable: "target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -258,7 +258,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs b/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs index 26bd0b50..bdeb8337 100755 --- a/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs +++ b/target/executable/metadata/move_obsm_to_obs/move_obsm_to_obs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_obsm_to_obs v4.0.1 +# move_obsm_to_obs v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component metadata move_obsm_to_obs" -LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:14Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_obsm_to_obs v4.0.1" + echo "move_obsm_to_obs v4.0.2" echo "" echo "Move a matrix from .obsm to .obs. Newly created columns in .obs will" echo "be created from the .obsm key suffixed with an underscore and the name of the" @@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_obsm_to_obs v4.0.1" + echo "move_obsm_to_obs v4.0.2" exit ;; --input) @@ -818,7 +818,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/move_obsm_to_obs:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/metadata/move_obsm_to_obs:v4.0.2' fi # print dockerfile diff --git a/target/executable/neighbors/bbknn/.config.vsh.yaml b/target/executable/neighbors/bbknn/.config.vsh.yaml index 25195ee3..ce71f881 100644 --- a/target/executable/neighbors/bbknn/.config.vsh.yaml +++ b/target/executable/neighbors/bbknn/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bbknn" namespace: "neighbors" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -272,7 +272,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -310,11 +310,11 @@ build_info: output: "target/executable/neighbors/bbknn" executable: "target/executable/neighbors/bbknn/bbknn" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -344,7 +344,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/neighbors/bbknn/bbknn b/target/executable/neighbors/bbknn/bbknn index 7a952bcd..985d22ff 100755 --- a/target/executable/neighbors/bbknn/bbknn +++ b/target/executable/neighbors/bbknn/bbknn @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bbknn v4.0.1 +# bbknn v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component neighbors bbknn" -LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:14Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bbknn v4.0.1" + echo "bbknn v4.0.2" echo "" echo "BBKNN network generation" echo "" @@ -702,7 +702,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bbknn v4.0.1" + echo "bbknn v4.0.2" exit ;; --input) @@ -937,7 +937,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/bbknn:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/bbknn:v4.0.2' fi # print dockerfile diff --git a/target/executable/neighbors/find_neighbors/.config.vsh.yaml b/target/executable/neighbors/find_neighbors/.config.vsh.yaml index ad9e08e9..e930fdd4 100644 --- a/target/executable/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/executable/neighbors/find_neighbors/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "find_neighbors" namespace: "neighbors" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -296,7 +296,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -338,11 +338,11 @@ build_info: output: "target/executable/neighbors/find_neighbors" executable: "target/executable/neighbors/find_neighbors/find_neighbors" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -372,7 +372,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/neighbors/find_neighbors/find_neighbors b/target/executable/neighbors/find_neighbors/find_neighbors index c6c2ca08..563e10fb 100755 --- a/target/executable/neighbors/find_neighbors/find_neighbors +++ b/target/executable/neighbors/find_neighbors/find_neighbors @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# find_neighbors v4.0.1 +# find_neighbors v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component neighbors find_neighbors" -LABEL org.opencontainers.image.created="2026-02-04T09:06:20Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:14Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "find_neighbors v4.0.1" + echo "find_neighbors v4.0.2" echo "" echo "Compute a neighborhood graph of observations [McInnes18]." echo "" @@ -707,7 +707,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "find_neighbors v4.0.1" + echo "find_neighbors v4.0.2" exit ;; --input) @@ -931,7 +931,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/find_neighbors:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/neighbors/find_neighbors:v4.0.2' fi # print dockerfile diff --git a/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml index c2ea4324..2fffabec 100644 --- a/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml +++ b/target/executable/process_10xh5/filter_10xh5/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_10xh5" namespace: "process_10xh5" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -182,7 +182,7 @@ engines: id: "docker" image: "eddelbuettel/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -226,11 +226,11 @@ build_info: output: "target/executable/process_10xh5/filter_10xh5" executable: "target/executable/process_10xh5/filter_10xh5/filter_10xh5" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -260,7 +260,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/process_10xh5/filter_10xh5/filter_10xh5 b/target/executable/process_10xh5/filter_10xh5/filter_10xh5 index d206378a..ef3b407a 100755 --- a/target/executable/process_10xh5/filter_10xh5/filter_10xh5 +++ b/target/executable/process_10xh5/filter_10xh5/filter_10xh5 @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# filter_10xh5 v4.0.1 +# filter_10xh5 v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -463,10 +463,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component process_10xh5 filter_10xh5" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -583,7 +583,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "filter_10xh5 v4.0.1" + echo "filter_10xh5 v4.0.2" echo "" echo "Filter a 10x h5 dataset." echo "" @@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "filter_10xh5 v4.0.1" + echo "filter_10xh5 v4.0.2" exit ;; --input) @@ -827,7 +827,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/process_10xh5/filter_10xh5:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/process_10xh5/filter_10xh5:v4.0.2' fi # print dockerfile diff --git a/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml b/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml index 9f64db0d..9708c53c 100644 --- a/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml +++ b/target/executable/qc/calculate_atac_qc_metrics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "calculate_atac_qc_metrics" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -249,7 +249,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -283,11 +283,11 @@ build_info: output: "target/executable/qc/calculate_atac_qc_metrics" executable: "target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -317,7 +317,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics b/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics index 4255b3d6..01c06498 100755 --- a/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics +++ b/target/executable/qc/calculate_atac_qc_metrics/calculate_atac_qc_metrics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# calculate_atac_qc_metrics v4.0.1 +# calculate_atac_qc_metrics v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component qc calculate_atac_qc_metrics" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "calculate_atac_qc_metrics v4.0.1" + echo "calculate_atac_qc_metrics v4.0.2" echo "" echo "Add basic ATAC quality control metrics to an .h5mu file." echo "" @@ -709,7 +709,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "calculate_atac_qc_metrics v4.0.1" + echo "calculate_atac_qc_metrics v4.0.2" exit ;; --input) @@ -910,7 +910,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_atac_qc_metrics:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_atac_qc_metrics:v4.0.2' fi # print dockerfile diff --git a/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml b/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml index ff10d909..6fa82395 100644 --- a/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/executable/qc/calculate_qc_metrics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "calculate_qc_metrics" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -295,7 +295,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -342,11 +342,11 @@ build_info: output: "target/executable/qc/calculate_qc_metrics" executable: "target/executable/qc/calculate_qc_metrics/calculate_qc_metrics" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -376,7 +376,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics b/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics index db5d24b7..704b4ca6 100755 --- a/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics +++ b/target/executable/qc/calculate_qc_metrics/calculate_qc_metrics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# calculate_qc_metrics v4.0.1 +# calculate_qc_metrics v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component qc calculate_qc_metrics" -LABEL org.opencontainers.image.created="2026-02-04T09:06:15Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "calculate_qc_metrics v4.0.1" + echo "calculate_qc_metrics v4.0.2" echo "" echo "Add basic quality control metrics to an .h5mu file." echo "" @@ -742,7 +742,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "calculate_qc_metrics v4.0.1" + echo "calculate_qc_metrics v4.0.2" exit ;; --input) @@ -999,7 +999,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_qc_metrics:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/calculate_qc_metrics:v4.0.2' fi # print dockerfile diff --git a/target/executable/qc/fastqc/.config.vsh.yaml b/target/executable/qc/fastqc/.config.vsh.yaml index 7f3e8eab..af006e4f 100644 --- a/target/executable/qc/fastqc/.config.vsh.yaml +++ b/target/executable/qc/fastqc/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "fastqc" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -158,7 +158,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -176,11 +176,11 @@ build_info: output: "target/executable/qc/fastqc" executable: "target/executable/qc/fastqc/fastqc" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -210,7 +210,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/qc/fastqc/fastqc b/target/executable/qc/fastqc/fastqc index f38e4abe..e8274e6c 100755 --- a/target/executable/qc/fastqc/fastqc +++ b/target/executable/qc/fastqc/fastqc @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# fastqc v4.0.1 +# fastqc v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component qc fastqc" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "fastqc v4.0.1" + echo "fastqc v4.0.2" echo "" echo "Fastqc component, please see" echo "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can" @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastqc v4.0.1" + echo "fastqc v4.0.2" exit ;; --mode) @@ -805,7 +805,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/fastqc:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/fastqc:v4.0.2' fi # print dockerfile diff --git a/target/executable/qc/multiqc/.config.vsh.yaml b/target/executable/qc/multiqc/.config.vsh.yaml index 6be2b165..7f0a86bf 100644 --- a/target/executable/qc/multiqc/.config.vsh.yaml +++ b/target/executable/qc/multiqc/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "multiqc" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -133,7 +133,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -162,11 +162,11 @@ build_info: output: "target/executable/qc/multiqc" executable: "target/executable/qc/multiqc/multiqc" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -196,7 +196,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/qc/multiqc/multiqc b/target/executable/qc/multiqc/multiqc index ec494eb7..b68d3c8b 100755 --- a/target/executable/qc/multiqc/multiqc +++ b/target/executable/qc/multiqc/multiqc @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# multiqc v4.0.1 +# multiqc v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "multiqc" LABEL org.opencontainers.image.description="Companion container for running component qc multiqc" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "multiqc v4.0.1" + echo "multiqc v4.0.2" echo "" echo "MultiQC aggregates results from bioinformatics analyses across many samples into" echo "a single report." @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multiqc v4.0.1" + echo "multiqc v4.0.2" exit ;; --input) @@ -773,7 +773,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/multiqc:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/qc/multiqc:v4.0.2' fi # print dockerfile diff --git a/target/executable/query/cellxgene_census/.config.vsh.yaml b/target/executable/query/cellxgene_census/.config.vsh.yaml index e1fc312c..0a197fb2 100644 --- a/target/executable/query/cellxgene_census/.config.vsh.yaml +++ b/target/executable/query/cellxgene_census/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellxgene_census" namespace: "query" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Matthias Beyens" roles: @@ -506,7 +506,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -539,11 +539,11 @@ build_info: output: "target/executable/query/cellxgene_census" executable: "target/executable/query/cellxgene_census/cellxgene_census" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -573,7 +573,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/query/cellxgene_census/cellxgene_census b/target/executable/query/cellxgene_census/cellxgene_census index 0e8e0e30..e0aeed41 100755 --- a/target/executable/query/cellxgene_census/cellxgene_census +++ b/target/executable/query/cellxgene_census/cellxgene_census @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellxgene_census v4.0.1 +# cellxgene_census v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Matthias Beyens, Dries De Maeyer, Robrecht Cannoodt, Kai Waldrant" LABEL org.opencontainers.image.description="Companion container for running component query cellxgene_census" -LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellxgene_census v4.0.1" + echo "cellxgene_census v4.0.2" echo "" echo "Query cells from a CellxGene Census or custom TileDBSoma object." echo "Aside from fetching the cells' RNA counts (\`.X\`), cell metadata" @@ -736,7 +736,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellxgene_census v4.0.1" + echo "cellxgene_census v4.0.2" exit ;; --input_uri) @@ -992,7 +992,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/cellxgene_census:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/cellxgene_census:v4.0.2' fi # print dockerfile diff --git a/target/executable/query/tiledb_healthcheck/.config.vsh.yaml b/target/executable/query/tiledb_healthcheck/.config.vsh.yaml index dad438fc..04211282 100644 --- a/target/executable/query/tiledb_healthcheck/.config.vsh.yaml +++ b/target/executable/query/tiledb_healthcheck/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tiledb_healthcheck" namespace: "query" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -137,7 +137,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -162,11 +162,11 @@ build_info: output: "target/executable/query/tiledb_healthcheck" executable: "target/executable/query/tiledb_healthcheck/tiledb_healthcheck" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -196,7 +196,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/query/tiledb_healthcheck/tiledb_healthcheck b/target/executable/query/tiledb_healthcheck/tiledb_healthcheck index 3fbfed73..51ba2d01 100755 --- a/target/executable/query/tiledb_healthcheck/tiledb_healthcheck +++ b/target/executable/query/tiledb_healthcheck/tiledb_healthcheck @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tiledb_healthcheck v4.0.1 +# tiledb_healthcheck v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component query tiledb_healthcheck" -LABEL org.opencontainers.image.created="2026-02-04T09:06:19Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:13Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tiledb_healthcheck v4.0.1" + echo "tiledb_healthcheck v4.0.2" echo "" echo "Checks if a provided location can be queried as a TileDB-SOMA database." echo "" @@ -636,7 +636,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tiledb_healthcheck v4.0.1" + echo "tiledb_healthcheck v4.0.2" exit ;; --input_uri) @@ -749,7 +749,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/tiledb_healthcheck:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/query/tiledb_healthcheck:v4.0.2' fi # print dockerfile diff --git a/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml b/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml index bf116f83..f3aa19e7 100644 --- a/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml +++ b/target/executable/reference/build_bdrhap_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_bdrhap_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -249,7 +249,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -274,11 +274,11 @@ build_info: output: "target/executable/reference/build_bdrhap_reference" executable: "target/executable/reference/build_bdrhap_reference/build_bdrhap_reference" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -308,7 +308,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference b/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference index 0a773fc0..17963511 100755 --- a/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference +++ b/target/executable/reference/build_bdrhap_reference/build_bdrhap_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# build_bdrhap_reference v4.0.1 +# build_bdrhap_reference v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component reference build_bdrhap_reference" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "build_bdrhap_reference v4.0.1" + echo "build_bdrhap_reference v4.0.2" echo "" echo "The Reference Files Generator creates an archive containing Genome Index" echo "and Transcriptome annotation files needed for the BD Rhapsody Sequencing" @@ -711,7 +711,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "build_bdrhap_reference v4.0.1" + echo "build_bdrhap_reference v4.0.2" exit ;; --genome_fasta) @@ -902,7 +902,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_bdrhap_reference:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_bdrhap_reference:v4.0.2' fi # print dockerfile diff --git a/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml b/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml index a5d47eeb..07078a03 100644 --- a/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml +++ b/target/executable/reference/build_cellranger_arc_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_cellranger_arc_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -213,7 +213,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger_arc:2.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -246,11 +246,11 @@ build_info: output: "target/executable/reference/build_cellranger_arc_reference" executable: "target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference b/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference index 23581b75..15b77acc 100755 --- a/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference +++ b/target/executable/reference/build_cellranger_arc_reference/build_cellranger_arc_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# build_cellranger_arc_reference v4.0.1 +# build_cellranger_arc_reference v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ apt upgrade -y && apt install -y procps pigz && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component reference build_cellranger_arc_reference" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "build_cellranger_arc_reference v4.0.1" + echo "build_cellranger_arc_reference v4.0.2" echo "" echo "Build a Cell Ranger-arc and -atac compatible reference folder from user-supplied" echo "genome FASTA and gene GTF files. Creates a new folder named after the genome." @@ -674,7 +674,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "build_cellranger_arc_reference v4.0.1" + echo "build_cellranger_arc_reference v4.0.2" exit ;; --genome_fasta) @@ -859,7 +859,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_arc_reference:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_arc_reference:v4.0.2' fi # print dockerfile diff --git a/target/executable/reference/build_cellranger_reference/.config.vsh.yaml b/target/executable/reference/build_cellranger_reference/.config.vsh.yaml index 183d3ec5..0a04e4fc 100644 --- a/target/executable/reference/build_cellranger_reference/.config.vsh.yaml +++ b/target/executable/reference/build_cellranger_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_cellranger_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -182,7 +182,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -214,11 +214,11 @@ build_info: output: "target/executable/reference/build_cellranger_reference" executable: "target/executable/reference/build_cellranger_reference/build_cellranger_reference" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -248,7 +248,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/reference/build_cellranger_reference/build_cellranger_reference b/target/executable/reference/build_cellranger_reference/build_cellranger_reference index 4414a9e6..33da813d 100755 --- a/target/executable/reference/build_cellranger_reference/build_cellranger_reference +++ b/target/executable/reference/build_cellranger_reference/build_cellranger_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# build_cellranger_reference v4.0.1 +# build_cellranger_reference v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ apt upgrade -y && apt install -y procps pigz && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference build_cellranger_reference" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "build_cellranger_reference v4.0.1" + echo "build_cellranger_reference v4.0.2" echo "" echo "Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA" echo "and gene GTF files. Creates a new folder named after the genome." @@ -646,7 +646,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "build_cellranger_reference v4.0.1" + echo "build_cellranger_reference v4.0.2" exit ;; --genome_fasta) @@ -781,7 +781,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_reference:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_cellranger_reference:v4.0.2' fi # print dockerfile diff --git a/target/executable/reference/build_star_reference/.config.vsh.yaml b/target/executable/reference/build_star_reference/.config.vsh.yaml index 61cd54de..bde104c0 100644 --- a/target/executable/reference/build_star_reference/.config.vsh.yaml +++ b/target/executable/reference/build_star_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_star_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -208,11 +208,11 @@ build_info: output: "target/executable/reference/build_star_reference" executable: "target/executable/reference/build_star_reference/build_star_reference" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -242,7 +242,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/reference/build_star_reference/build_star_reference b/target/executable/reference/build_star_reference/build_star_reference index 46ccf74a..12d9bfe5 100755 --- a/target/executable/reference/build_star_reference/build_star_reference +++ b/target/executable/reference/build_star_reference/build_star_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# build_star_reference v4.0.1 +# build_star_reference v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -469,10 +469,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component reference build_star_reference" -LABEL org.opencontainers.image.created="2026-02-04T09:06:27Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -589,7 +589,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "build_star_reference v4.0.1" + echo "build_star_reference v4.0.2" echo "" echo "Create a reference for STAR from a set of fasta files." echo "" @@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "build_star_reference v4.0.1" + echo "build_star_reference v4.0.2" exit ;; --genome_fasta) @@ -835,7 +835,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_star_reference:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/build_star_reference:v4.0.2' fi # print dockerfile diff --git a/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml b/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml index 04f46f20..785717cb 100644 --- a/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml +++ b/target/executable/reference/cellranger_mkgtf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mkgtf" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -152,7 +152,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -182,11 +182,11 @@ build_info: output: "target/executable/reference/cellranger_mkgtf" executable: "target/executable/reference/cellranger_mkgtf/cellranger_mkgtf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -216,7 +216,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf b/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf index b22b257b..8ae9db21 100755 --- a/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf +++ b/target/executable/reference/cellranger_mkgtf/cellranger_mkgtf @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# cellranger_mkgtf v4.0.1 +# cellranger_mkgtf v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ apt upgrade -y && apt install -y pigz procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component reference cellranger_mkgtf" -LABEL org.opencontainers.image.created="2026-02-04T09:06:28Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:22Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "cellranger_mkgtf v4.0.1" + echo "cellranger_mkgtf v4.0.2" echo "" echo "Make a GTF file - filter by a specific attribute." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cellranger_mkgtf v4.0.1" + echo "cellranger_mkgtf v4.0.2" exit ;; --input_gtf) @@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/cellranger_mkgtf:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/cellranger_mkgtf:v4.0.2' fi # print dockerfile diff --git a/target/executable/reference/make_reference/.config.vsh.yaml b/target/executable/reference/make_reference/.config.vsh.yaml index 8ff85d50..4c96098a 100644 --- a/target/executable/reference/make_reference/.config.vsh.yaml +++ b/target/executable/reference/make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "make_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -231,11 +231,11 @@ build_info: output: "target/executable/reference/make_reference" executable: "target/executable/reference/make_reference/make_reference" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -265,7 +265,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/reference/make_reference/make_reference b/target/executable/reference/make_reference/make_reference index b716e3dd..6d877403 100755 --- a/target/executable/reference/make_reference/make_reference +++ b/target/executable/reference/make_reference/make_reference @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# make_reference v4.0.1 +# make_reference v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Angela Oliveira Pisco, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component reference make_reference" -LABEL org.opencontainers.image.created="2026-02-04T09:06:26Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:21Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "make_reference v4.0.1" + echo "make_reference v4.0.2" echo "" echo "Preprocess and build a transcriptome reference." echo "" @@ -664,7 +664,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "make_reference v4.0.1" + echo "make_reference v4.0.2" exit ;; --genome_fasta) @@ -821,7 +821,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/make_reference:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/reference/make_reference:v4.0.2' fi # print dockerfile diff --git a/target/executable/report/mermaid/.config.vsh.yaml b/target/executable/report/mermaid/.config.vsh.yaml index 6fadeb13..81f60d06 100644 --- a/target/executable/report/mermaid/.config.vsh.yaml +++ b/target/executable/report/mermaid/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "mermaid" namespace: "report" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -182,7 +182,7 @@ engines: id: "docker" image: "node:20-bullseye" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "javascript" @@ -203,11 +203,11 @@ build_info: output: "target/executable/report/mermaid" executable: "target/executable/report/mermaid/mermaid" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -237,7 +237,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/report/mermaid/mermaid b/target/executable/report/mermaid/mermaid index d70ec223..e05c76e4 100755 --- a/target/executable/report/mermaid/mermaid +++ b/target/executable/report/mermaid/mermaid @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# mermaid v4.0.1 +# mermaid v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -456,10 +456,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Dries De Maeyer" LABEL org.opencontainers.image.description="Companion container for running component report mermaid" -LABEL org.opencontainers.image.created="2026-02-04T09:06:09Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:04Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "mermaid v4.0.1" + echo "mermaid v4.0.2" echo "" echo "Generates a network from mermaid code." echo "" @@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "mermaid v4.0.1" + echo "mermaid v4.0.2" exit ;; --input) @@ -828,7 +828,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/report/mermaid:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/report/mermaid:v4.0.2' fi # print dockerfile diff --git a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml index adf496d7..7ff877c1 100644 --- a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml +++ b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "assert_test_workflow_2_output" namespace: "test_workflows/multiomics/process_samples" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" info: @@ -136,7 +136,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -169,11 +169,11 @@ build_info: output: "target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output" executable: "target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -203,7 +203,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output index f9796933..65e1cafc 100755 --- a/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output +++ b/target/executable/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/assert_test_workflow_2_output @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# assert_test_workflow_2_output v4.0.1 +# assert_test_workflow_2_output v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/multiomics/process_samples assert_test_workflow_2_output" -LABEL org.opencontainers.image.created="2026-02-04T09:06:25Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:19Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "assert_test_workflow_2_output v4.0.1" + echo "assert_test_workflow_2_output v4.0.2" echo "" echo "This component tests the output of the integration test of process_samples" echo "test_wf." @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "assert_test_workflow_2_output v4.0.1" + echo "assert_test_workflow_2_output v4.0.2" exit ;; --input) @@ -760,7 +760,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_samples/assert_test_workflow_2_output:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/test_workflows/multiomics/process_samples/assert_test_workflow_2_output:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/bpcells_regress_out/.config.vsh.yaml b/target/executable/transform/bpcells_regress_out/.config.vsh.yaml index 2920f1b7..aa9487e6 100644 --- a/target/executable/transform/bpcells_regress_out/.config.vsh.yaml +++ b/target/executable/transform/bpcells_regress_out/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bpcells_regress_out" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -284,11 +284,11 @@ build_info: output: "target/executable/transform/bpcells_regress_out" executable: "target/executable/transform/bpcells_regress_out/bpcells_regress_out" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -318,7 +318,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/bpcells_regress_out/bpcells_regress_out b/target/executable/transform/bpcells_regress_out/bpcells_regress_out index 50a40742..4f112b98 100755 --- a/target/executable/transform/bpcells_regress_out/bpcells_regress_out +++ b/target/executable/transform/bpcells_regress_out/bpcells_regress_out @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bpcells_regress_out v4.0.1 +# bpcells_regress_out v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -467,10 +467,10 @@ RUN pip install --user --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component transform bpcells_regress_out" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -587,7 +587,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bpcells_regress_out v4.0.1" + echo "bpcells_regress_out v4.0.2" echo "" echo "Regress out the effects of confounding variables using a linear least squares" echo "regression model with BPCells." @@ -678,7 +678,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bpcells_regress_out v4.0.1" + echo "bpcells_regress_out v4.0.2" exit ;; --input) @@ -858,7 +858,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/bpcells_regress_out:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/bpcells_regress_out:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/clr/.config.vsh.yaml b/target/executable/transform/clr/.config.vsh.yaml index a0c2d124..4ec95800 100644 --- a/target/executable/transform/clr/.config.vsh.yaml +++ b/target/executable/transform/clr/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "clr" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -203,7 +203,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -240,11 +240,11 @@ build_info: output: "target/executable/transform/clr" executable: "target/executable/transform/clr/clr" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -274,7 +274,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/clr/clr b/target/executable/transform/clr/clr index c507c0c0..c59b9c83 100755 --- a/target/executable/transform/clr/clr +++ b/target/executable/transform/clr/clr @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# clr v4.0.1 +# clr v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform clr" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "clr v4.0.1" + echo "clr v4.0.2" echo "" echo "Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017)." echo "" @@ -668,7 +668,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "clr v4.0.1" + echo "clr v4.0.2" exit ;; --input) @@ -848,7 +848,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/clr:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/clr:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/delete_layer/.config.vsh.yaml b/target/executable/transform/delete_layer/.config.vsh.yaml index 38715983..3877c345 100644 --- a/target/executable/transform/delete_layer/.config.vsh.yaml +++ b/target/executable/transform/delete_layer/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "delete_layer" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -186,7 +186,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -227,11 +227,11 @@ build_info: output: "target/executable/transform/delete_layer" executable: "target/executable/transform/delete_layer/delete_layer" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -261,7 +261,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/delete_layer/delete_layer b/target/executable/transform/delete_layer/delete_layer index 3f163983..7f4960e7 100755 --- a/target/executable/transform/delete_layer/delete_layer +++ b/target/executable/transform/delete_layer/delete_layer @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# delete_layer v4.0.1 +# delete_layer v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform delete_layer" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "delete_layer v4.0.1" + echo "delete_layer v4.0.2" echo "" echo "Delete an anndata layer from one or more modalities." echo "" @@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "delete_layer v4.0.1" + echo "delete_layer v4.0.2" exit ;; --input) @@ -829,7 +829,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/delete_layer:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/delete_layer:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/log1p/.config.vsh.yaml b/target/executable/transform/log1p/.config.vsh.yaml index 2c539465..a59fa936 100644 --- a/target/executable/transform/log1p/.config.vsh.yaml +++ b/target/executable/transform/log1p/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "log1p" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -217,7 +217,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -253,11 +253,11 @@ build_info: output: "target/executable/transform/log1p" executable: "target/executable/transform/log1p/log1p" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -287,7 +287,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/log1p/log1p b/target/executable/transform/log1p/log1p index 14d238f0..23d9b9ab 100755 --- a/target/executable/transform/log1p/log1p +++ b/target/executable/transform/log1p/log1p @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# log1p v4.0.1 +# log1p v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform log1p" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "log1p v4.0.1" + echo "log1p v4.0.2" echo "" echo "Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the" echo "natural logarithm unless a different base is given." @@ -667,7 +667,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "log1p v4.0.1" + echo "log1p v4.0.2" exit ;; --input) @@ -847,7 +847,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/log1p:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/log1p:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/move_layer/.config.vsh.yaml b/target/executable/transform/move_layer/.config.vsh.yaml index 23f46d3e..c43341e8 100644 --- a/target/executable/transform/move_layer/.config.vsh.yaml +++ b/target/executable/transform/move_layer/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_layer" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -176,7 +176,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -217,11 +217,11 @@ build_info: output: "target/executable/transform/move_layer" executable: "target/executable/transform/move_layer/move_layer" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -251,7 +251,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/move_layer/move_layer b/target/executable/transform/move_layer/move_layer index 7a43fafd..a184a78e 100755 --- a/target/executable/transform/move_layer/move_layer +++ b/target/executable/transform/move_layer/move_layer @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# move_layer v4.0.1 +# move_layer v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ RUN pip install --upgrade pip && \ python -c 'exec("try:\n import zarr; from importlib.metadata import version\nexcept ModuleNotFoundError:\n exit(0)\nelse: assert int(version(\"zarr\").partition(\".\")[0]) > 2")' LABEL org.opencontainers.image.description="Companion container for running component transform move_layer" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "move_layer v4.0.1" + echo "move_layer v4.0.2" echo "" echo "Move a data matrix stored at the .layers or .X attributes in a MuData object to" echo "another layer." @@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "move_layer v4.0.1" + echo "move_layer v4.0.2" exit ;; --input) @@ -830,7 +830,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/move_layer:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/move_layer:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/normalize_total/.config.vsh.yaml b/target/executable/transform/normalize_total/.config.vsh.yaml index 5fd4c6d3..cc7c1603 100644 --- a/target/executable/transform/normalize_total/.config.vsh.yaml +++ b/target/executable/transform/normalize_total/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "normalize_total" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -229,7 +229,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -271,11 +271,11 @@ build_info: output: "target/executable/transform/normalize_total" executable: "target/executable/transform/normalize_total/normalize_total" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -305,7 +305,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/normalize_total/normalize_total b/target/executable/transform/normalize_total/normalize_total index a6e7879c..2336fd0a 100755 --- a/target/executable/transform/normalize_total/normalize_total +++ b/target/executable/transform/normalize_total/normalize_total @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# normalize_total v4.0.1 +# normalize_total v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -459,10 +459,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries De Maeyer, Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform normalize_total" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -579,7 +579,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "normalize_total v4.0.1" + echo "normalize_total v4.0.2" echo "" echo "Normalize counts per cell." echo "" @@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "normalize_total v4.0.1" + echo "normalize_total v4.0.2" exit ;; --input) @@ -868,7 +868,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/normalize_total:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/normalize_total:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/regress_out/.config.vsh.yaml b/target/executable/transform/regress_out/.config.vsh.yaml index b19e29de..3573e66a 100644 --- a/target/executable/transform/regress_out/.config.vsh.yaml +++ b/target/executable/transform/regress_out/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "regress_out" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -206,7 +206,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -248,11 +248,11 @@ build_info: output: "target/executable/transform/regress_out" executable: "target/executable/transform/regress_out/regress_out" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -282,7 +282,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/regress_out/regress_out b/target/executable/transform/regress_out/regress_out index bf4b367f..577f95d5 100755 --- a/target/executable/transform/regress_out/regress_out +++ b/target/executable/transform/regress_out/regress_out @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# regress_out v4.0.1 +# regress_out v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component transform regress_out" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "regress_out v4.0.1" + echo "regress_out v4.0.2" echo "" echo "Regress out (mostly) unwanted sources of variation." echo "Uses simple linear regression. This is inspired by Seurat's regressOut function" @@ -673,7 +673,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "regress_out v4.0.1" + echo "regress_out v4.0.2" exit ;; --input) @@ -853,7 +853,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/regress_out:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/regress_out:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/scale/.config.vsh.yaml b/target/executable/transform/scale/.config.vsh.yaml index e5f21701..508c21bc 100644 --- a/target/executable/transform/scale/.config.vsh.yaml +++ b/target/executable/transform/scale/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scale" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -204,7 +204,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -246,11 +246,11 @@ build_info: output: "target/executable/transform/scale" executable: "target/executable/transform/scale/scale" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/scale/scale b/target/executable/transform/scale/scale index 92bcd658..98cb0c5c 100755 --- a/target/executable/transform/scale/scale +++ b/target/executable/transform/scale/scale @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scale v4.0.1 +# scale v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component transform scale" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:11Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scale v4.0.1" + echo "scale v4.0.2" echo "" echo "Scale data to unit variance and zero mean." echo "" @@ -670,7 +670,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scale v4.0.1" + echo "scale v4.0.2" exit ;; --input) @@ -855,7 +855,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/scale:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/scale:v4.0.2' fi # print dockerfile diff --git a/target/executable/transform/tfidf/.config.vsh.yaml b/target/executable/transform/tfidf/.config.vsh.yaml index d21f1b50..aec4768d 100644 --- a/target/executable/transform/tfidf/.config.vsh.yaml +++ b/target/executable/transform/tfidf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tfidf" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -237,7 +237,7 @@ engines: id: "docker" image: "python:3.13-slim-bullseye" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -277,11 +277,11 @@ build_info: output: "target/executable/transform/tfidf" executable: "target/executable/transform/tfidf/tfidf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -311,7 +311,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/transform/tfidf/tfidf b/target/executable/transform/tfidf/tfidf index f097cdb5..7714519d 100755 --- a/target/executable/transform/tfidf/tfidf +++ b/target/executable/transform/tfidf/tfidf @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# tfidf v4.0.1 +# tfidf v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Vladimir Shitov" LABEL org.opencontainers.image.description="Companion container for running component transform tfidf" -LABEL org.opencontainers.image.created="2026-02-04T09:06:16Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:10Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "tfidf v4.0.1" + echo "tfidf v4.0.2" echo "" echo "Perform TF-IDF normalization of the data (typically, ATAC)." echo "" @@ -691,7 +691,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tfidf v4.0.1" + echo "tfidf v4.0.2" exit ;; --input) @@ -904,7 +904,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/tfidf:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/transform/tfidf:v4.0.2' fi # print dockerfile diff --git a/target/executable/velocity/scvelo/.config.vsh.yaml b/target/executable/velocity/scvelo/.config.vsh.yaml index c5e033a3..c9492022 100644 --- a/target/executable/velocity/scvelo/.config.vsh.yaml +++ b/target/executable/velocity/scvelo/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvelo" namespace: "velocity" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -311,7 +311,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -356,11 +356,11 @@ build_info: output: "target/executable/velocity/scvelo" executable: "target/executable/velocity/scvelo/scvelo" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -390,7 +390,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/velocity/scvelo/scvelo b/target/executable/velocity/scvelo/scvelo index bb7172ac..ad3719b3 100755 --- a/target/executable/velocity/scvelo/scvelo +++ b/target/executable/velocity/scvelo/scvelo @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# scvelo v4.0.1 +# scvelo v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component velocity scvelo" -LABEL org.opencontainers.image.created="2026-02-04T09:06:17Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "scvelo v4.0.1" + echo "scvelo v4.0.2" echo "" echo "Inputs:" echo " --input" @@ -734,7 +734,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "scvelo v4.0.1" + echo "scvelo v4.0.2" exit ;; --input) @@ -1034,7 +1034,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/scvelo:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/scvelo:v4.0.2' fi # print dockerfile diff --git a/target/executable/velocity/velocyto/.config.vsh.yaml b/target/executable/velocity/velocyto/.config.vsh.yaml index d7658edf..42b89133 100644 --- a/target/executable/velocity/velocyto/.config.vsh.yaml +++ b/target/executable/velocity/velocyto/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "velocyto" namespace: "velocity" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -202,7 +202,7 @@ engines: id: "docker" image: "python:3.13" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -246,11 +246,11 @@ build_info: output: "target/executable/velocity/velocyto" executable: "target/executable/velocity/velocyto/velocyto" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/executable/velocity/velocyto/velocyto b/target/executable/velocity/velocyto/velocyto index 17e72693..267919db 100755 --- a/target/executable/velocity/velocyto/velocyto +++ b/target/executable/velocity/velocyto/velocyto @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# velocyto v4.0.1 +# velocyto v4.0.2 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -464,10 +464,10 @@ RUN apt-get update && \ LABEL org.opencontainers.image.authors="Robrecht Cannoodt" LABEL org.opencontainers.image.description="Companion container for running component velocity velocyto" -LABEL org.opencontainers.image.created="2026-02-04T09:06:18Z" +LABEL org.opencontainers.image.created="2026-02-11T14:34:12Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline" -LABEL org.opencontainers.image.revision="e943ae3d1512ded126303c9481cb554d0dd38c92" -LABEL org.opencontainers.image.version="v4.0.1" +LABEL org.opencontainers.image.revision="cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" +LABEL org.opencontainers.image.version="v4.0.2" VIASHDOCKER fi @@ -584,7 +584,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "velocyto v4.0.1" + echo "velocyto v4.0.2" echo "" echo "Runs the velocity analysis on a BAM file, outputting a loom file." echo "" @@ -666,7 +666,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "velocyto v4.0.1" + echo "velocyto v4.0.2" exit ;; --input) @@ -847,7 +847,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/velocyto:v4.0.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/openpipeline/velocity/velocyto:v4.0.2' fi # print dockerfile diff --git a/target/nextflow/annotate/celltypist/.config.vsh.yaml b/target/nextflow/annotate/celltypist/.config.vsh.yaml index b3ff58a4..488e9a82 100644 --- a/target/nextflow/annotate/celltypist/.config.vsh.yaml +++ b/target/nextflow/annotate/celltypist/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "celltypist" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -384,7 +384,7 @@ engines: id: "docker" image: "nvcr.io/nvidia/pytorch:25.11-py3" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -431,11 +431,11 @@ build_info: output: "target/nextflow/annotate/celltypist" executable: "target/nextflow/annotate/celltypist/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -465,7 +465,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/celltypist/main.nf b/target/nextflow/annotate/celltypist/main.nf index 1f0af76d..6db2b208 100644 --- a/target/nextflow/annotate/celltypist/main.nf +++ b/target/nextflow/annotate/celltypist/main.nf @@ -1,4 +1,4 @@ -// celltypist v4.0.1 +// celltypist v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "celltypist", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3507,7 +3507,7 @@ meta = [ "id" : "docker", "image" : "nvcr.io/nvidia/pytorch:25.11-py3", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3572,12 +3572,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/celltypist", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3602,7 +3602,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4200,7 +4200,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/celltypist", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/annotate/celltypist/nextflow.config b/target/nextflow/annotate/celltypist/nextflow.config index 01e740bd..d22190c4 100644 --- a/target/nextflow/annotate/celltypist/nextflow.config +++ b/target/nextflow/annotate/celltypist/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/celltypist' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm.' author = 'Jakub Majercik, Weiwei Schultz' } diff --git a/target/nextflow/annotate/onclass/.config.vsh.yaml b/target/nextflow/annotate/onclass/.config.vsh.yaml index d169157e..b65ddf4f 100644 --- a/target/nextflow/annotate/onclass/.config.vsh.yaml +++ b/target/nextflow/annotate/onclass/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "onclass" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -365,7 +365,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -405,11 +405,11 @@ build_info: output: "target/nextflow/annotate/onclass" executable: "target/nextflow/annotate/onclass/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -439,7 +439,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/onclass/main.nf b/target/nextflow/annotate/onclass/main.nf index 0d1130ac..8f612b7f 100644 --- a/target/nextflow/annotate/onclass/main.nf +++ b/target/nextflow/annotate/onclass/main.nf @@ -1,4 +1,4 @@ -// onclass v4.0.1 +// onclass v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "onclass", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3478,7 +3478,7 @@ meta = [ "id" : "docker", "image" : "python:3.11", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3530,12 +3530,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/onclass", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3560,7 +3560,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4211,7 +4211,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/onclass", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/annotate/onclass/nextflow.config b/target/nextflow/annotate/onclass/nextflow.config index ce108a78..81ff8800 100644 --- a/target/nextflow/annotate/onclass/nextflow.config +++ b/target/nextflow/annotate/onclass/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/onclass' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'OnClass is a python package for single-cell cell type annotation. It uses the Cell Ontology to capture the cell type similarity. \nThese similarities enable OnClass to annotate cell types that are never seen in the training data.\n' author = 'Jakub Majercik' } diff --git a/target/nextflow/annotate/popv/.config.vsh.yaml b/target/nextflow/annotate/popv/.config.vsh.yaml index b78451d3..88a8c134 100644 --- a/target/nextflow/annotate/popv/.config.vsh.yaml +++ b/target/nextflow/annotate/popv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "popv" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Matthias Beyens" roles: @@ -310,7 +310,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -361,11 +361,11 @@ build_info: output: "target/nextflow/annotate/popv" executable: "target/nextflow/annotate/popv/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -395,7 +395,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/popv/main.nf b/target/nextflow/annotate/popv/main.nf index 55cf6801..9759a358 100644 --- a/target/nextflow/annotate/popv/main.nf +++ b/target/nextflow/annotate/popv/main.nf @@ -1,4 +1,4 @@ -// popv v4.0.1 +// popv v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "popv", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Matthias Beyens", @@ -3421,7 +3421,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3492,12 +3492,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/popv", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3522,7 +3522,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4172,7 +4172,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/popv", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/annotate/popv/nextflow.config b/target/nextflow/annotate/popv/nextflow.config index 5ea1d455..ef136d38 100644 --- a/target/nextflow/annotate/popv/nextflow.config +++ b/target/nextflow/annotate/popv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/popv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs popular major vote cell typing on single cell sequence data using multiple algorithms. Note that this is a one-shot version of PopV.' author = 'Matthias Beyens, Robrecht Cannoodt' } diff --git a/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml b/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml index 01c22e05..d8d88f41 100644 --- a/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml +++ b/target/nextflow/annotate/random_forest_annotation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "random_forest_annotation" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -373,7 +373,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -420,11 +420,11 @@ build_info: output: "target/nextflow/annotate/random_forest_annotation" executable: "target/nextflow/annotate/random_forest_annotation/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -454,7 +454,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/random_forest_annotation/main.nf b/target/nextflow/annotate/random_forest_annotation/main.nf index e1f01208..523af01e 100644 --- a/target/nextflow/annotate/random_forest_annotation/main.nf +++ b/target/nextflow/annotate/random_forest_annotation/main.nf @@ -1,4 +1,4 @@ -// random_forest_annotation v4.0.1 +// random_forest_annotation v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "random_forest_annotation", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3481,7 +3481,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3546,12 +3546,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/random_forest_annotation", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3576,7 +3576,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4171,7 +4171,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/random_forest_annotation", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/annotate/random_forest_annotation/nextflow.config b/target/nextflow/annotate/random_forest_annotation/nextflow.config index 3d784e80..cbf0e341 100644 --- a/target/nextflow/annotate/random_forest_annotation/nextflow.config +++ b/target/nextflow/annotate/random_forest_annotation/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/random_forest_annotation' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Automated cell type annotation tool for scRNA-seq datasets on the basis of random forest.' author = 'Jakub Majercik' } diff --git a/target/nextflow/annotate/scanvi/.config.vsh.yaml b/target/nextflow/annotate/scanvi/.config.vsh.yaml index dbc085ac..7da799f6 100644 --- a/target/nextflow/annotate/scanvi/.config.vsh.yaml +++ b/target/nextflow/annotate/scanvi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanvi" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -405,7 +405,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -442,11 +442,11 @@ build_info: output: "target/nextflow/annotate/scanvi" executable: "target/nextflow/annotate/scanvi/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -476,7 +476,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/scanvi/main.nf b/target/nextflow/annotate/scanvi/main.nf index 624d204b..ccb5f5a2 100644 --- a/target/nextflow/annotate/scanvi/main.nf +++ b/target/nextflow/annotate/scanvi/main.nf @@ -1,4 +1,4 @@ -// scanvi v4.0.1 +// scanvi v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scanvi", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3542,7 +3542,7 @@ meta = [ "id" : "docker", "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3590,12 +3590,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/scanvi", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3620,7 +3620,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4170,7 +4170,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/scanvi", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midcpu", diff --git a/target/nextflow/annotate/scanvi/nextflow.config b/target/nextflow/annotate/scanvi/nextflow.config index 25ca04dd..ea909c98 100644 --- a/target/nextflow/annotate/scanvi/nextflow.config +++ b/target/nextflow/annotate/scanvi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/scanvi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'scANVI () is a semi-supervised model for single-cell transcriptomics data. scANVI is an scVI extension that can leverage the cell type knowledge for a subset of the cells present in the data sets to infer the states of the rest of the cells.\nThis component will instantiate a scANVI model from a pre-trained scVI model, integrate the data and perform label prediction.\n' author = 'Dorien Roosen, Jakub Majercik, Weiwei Schultz' } diff --git a/target/nextflow/annotate/singler/.config.vsh.yaml b/target/nextflow/annotate/singler/.config.vsh.yaml index 171380f3..0b61eae5 100644 --- a/target/nextflow/annotate/singler/.config.vsh.yaml +++ b/target/nextflow/annotate/singler/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "singler" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -424,7 +424,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -483,11 +483,11 @@ build_info: output: "target/nextflow/annotate/singler" executable: "target/nextflow/annotate/singler/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -517,7 +517,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/singler/main.nf b/target/nextflow/annotate/singler/main.nf index 29e90424..071c3eff 100644 --- a/target/nextflow/annotate/singler/main.nf +++ b/target/nextflow/annotate/singler/main.nf @@ -1,4 +1,4 @@ -// singler v4.0.1 +// singler v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "singler", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3524,7 +3524,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3605,12 +3605,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/singler", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3635,7 +3635,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4277,7 +4277,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/singler", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/annotate/singler/nextflow.config b/target/nextflow/annotate/singler/nextflow.config index 215c4f92..f122923f 100644 --- a/target/nextflow/annotate/singler/nextflow.config +++ b/target/nextflow/annotate/singler/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/singler' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'SingleR performs reference-based cell type annotation for single-cell RNA-seq data \nby computing Spearman correlations between test cells and reference samples with known labels, \nusing marker genes to assign the most similar cell type label to each new cell.\n' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/annotate/svm_annotation/.config.vsh.yaml b/target/nextflow/annotate/svm_annotation/.config.vsh.yaml index 536c9721..1c6f4ad1 100644 --- a/target/nextflow/annotate/svm_annotation/.config.vsh.yaml +++ b/target/nextflow/annotate/svm_annotation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "svm_annotation" namespace: "annotate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -356,7 +356,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -403,11 +403,11 @@ build_info: output: "target/nextflow/annotate/svm_annotation" executable: "target/nextflow/annotate/svm_annotation/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -437,7 +437,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/annotate/svm_annotation/main.nf b/target/nextflow/annotate/svm_annotation/main.nf index c446935a..b7d2108b 100644 --- a/target/nextflow/annotate/svm_annotation/main.nf +++ b/target/nextflow/annotate/svm_annotation/main.nf @@ -1,4 +1,4 @@ -// svm_annotation v4.0.1 +// svm_annotation v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "svm_annotation", "namespace" : "annotate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3468,7 +3468,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3533,12 +3533,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/annotate/svm_annotation", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3563,7 +3563,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4141,7 +4141,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/annotate/svm_annotation", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/annotate/svm_annotation/nextflow.config b/target/nextflow/annotate/svm_annotation/nextflow.config index f4ff1f6f..15ab0253 100644 --- a/target/nextflow/annotate/svm_annotation/nextflow.config +++ b/target/nextflow/annotate/svm_annotation/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'annotate/svm_annotation' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Automated cell type annotation tool for scRNA-seq datasets on the basis of SVMs.' author = 'Jakub Majercik' } diff --git a/target/nextflow/cluster/leiden/.config.vsh.yaml b/target/nextflow/cluster/leiden/.config.vsh.yaml index 68a1032d..e9d7e495 100644 --- a/target/nextflow/cluster/leiden/.config.vsh.yaml +++ b/target/nextflow/cluster/leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "leiden" namespace: "cluster" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -215,7 +215,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -258,11 +258,11 @@ build_info: output: "target/nextflow/cluster/leiden" executable: "target/nextflow/cluster/leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/cluster/leiden/main.nf b/target/nextflow/cluster/leiden/main.nf index ba1c8c67..6a5f549d 100644 --- a/target/nextflow/cluster/leiden/main.nf +++ b/target/nextflow/cluster/leiden/main.nf @@ -1,4 +1,4 @@ -// leiden v4.0.1 +// leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "leiden", "namespace" : "cluster", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3294,7 +3294,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3352,12 +3352,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cluster/leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3382,7 +3382,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4147,7 +4147,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/cluster/leiden", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/cluster/leiden/nextflow.config b/target/nextflow/cluster/leiden/nextflow.config index 83a52fd5..bb4c68de 100644 --- a/target/nextflow/cluster/leiden/nextflow.config +++ b/target/nextflow/cluster/leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'cluster/leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Cluster cells using the [Leiden algorithm] [Traag18] implemented in the [Scanpy framework] [Wolf18]. \nLeiden is an improved version of the [Louvain algorithm] [Blondel08]. \nIt has been proposed for single-cell analysis by [Levine15] [Levine15]. \nThis requires having ran `neighbors/find_neighbors` or `neighbors/bbknn` first.\n\n[Blondel08]: Blondel et al. (2008), Fast unfolding of communities in large networks, J. Stat. Mech. \n[Levine15]: Levine et al. (2015), Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis, Cell. \n[Traag18]: Traag et al. (2018), From Louvain to Leiden: guaranteeing well-connected communities arXiv. \n[Wolf18]: Wolf et al. (2018), Scanpy: large-scale single-cell gene expression data analysis, Genome Biology. \n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml index 1cd1ae52..2990d81f 100644 --- a/target/nextflow/compression/compress_h5mu/.config.vsh.yaml +++ b/target/nextflow/compression/compress_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "compress_h5mu" namespace: "compression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -157,7 +157,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,11 @@ build_info: output: "target/nextflow/compression/compress_h5mu" executable: "target/nextflow/compression/compress_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -232,7 +232,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/compression/compress_h5mu/main.nf b/target/nextflow/compression/compress_h5mu/main.nf index b3d7dbc4..19e8bb14 100644 --- a/target/nextflow/compression/compress_h5mu/main.nf +++ b/target/nextflow/compression/compress_h5mu/main.nf @@ -1,4 +1,4 @@ -// compress_h5mu v4.0.1 +// compress_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "compress_h5mu", "namespace" : "compression", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3236,7 +3236,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3292,12 +3292,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/compression/compress_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3322,7 +3322,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3772,7 +3772,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/compression/compress_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/compression/compress_h5mu/nextflow.config b/target/nextflow/compression/compress_h5mu/nextflow.config index 4ccc42ed..60981dee 100644 --- a/target/nextflow/compression/compress_h5mu/nextflow.config +++ b/target/nextflow/compression/compress_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'compression/compress_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Compress a MuData file. \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/compression/tar_extract/.config.vsh.yaml b/target/nextflow/compression/tar_extract/.config.vsh.yaml index f6155a66..355e8a94 100644 --- a/target/nextflow/compression/tar_extract/.config.vsh.yaml +++ b/target/nextflow/compression/tar_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tar_extract" namespace: "compression" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -157,7 +157,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -170,11 +170,11 @@ build_info: output: "target/nextflow/compression/tar_extract" executable: "target/nextflow/compression/tar_extract/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -204,7 +204,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/compression/tar_extract/main.nf b/target/nextflow/compression/tar_extract/main.nf index 32b7356f..4b49fbb5 100644 --- a/target/nextflow/compression/tar_extract/main.nf +++ b/target/nextflow/compression/tar_extract/main.nf @@ -1,4 +1,4 @@ -// tar_extract v4.0.1 +// tar_extract v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "tar_extract", "namespace" : "compression", - "version" : "v4.0.1", + "version" : "v4.0.2", "argument_groups" : [ { "name" : "Arguments", @@ -3225,7 +3225,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/" }, { @@ -3239,12 +3239,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/compression/tar_extract", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3269,7 +3269,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3722,7 +3722,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/compression/tar_extract", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/compression/tar_extract/nextflow.config b/target/nextflow/compression/tar_extract/nextflow.config index 8c7da9f7..7af6ba1f 100644 --- a/target/nextflow/compression/tar_extract/nextflow.config +++ b/target/nextflow/compression/tar_extract/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'compression/tar_extract' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Extract files from a tar archive' } diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml index 068def9c..6821ab79 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_10xh5_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_10xh5_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -263,7 +263,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -305,11 +305,11 @@ build_info: output: "target/nextflow/convert/from_10xh5_to_h5mu" executable: "target/nextflow/convert/from_10xh5_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -339,7 +339,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf index b555eee0..616cdc98 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/main.nf +++ b/target/nextflow/convert/from_10xh5_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_10xh5_to_h5mu v4.0.1 +// from_10xh5_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_10xh5_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3394,7 +3394,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3451,12 +3451,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_10xh5_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3481,7 +3481,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3988,7 +3988,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_10xh5_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config b/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config index c545bcaf..e587cd5e 100644 --- a/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_10xh5_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_10xh5_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts a 10x h5 into an h5mu file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml index d9e96736..0feb27db 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_10xmtx_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -164,7 +164,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -206,11 +206,11 @@ build_info: output: "target/nextflow/convert/from_10xmtx_to_h5mu" executable: "target/nextflow/convert/from_10xmtx_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -240,7 +240,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf index f8708724..12505089 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_10xmtx_to_h5mu v4.0.1 +// from_10xmtx_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_10xmtx_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3247,7 +3247,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3304,12 +3304,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_10xmtx_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3334,7 +3334,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3802,7 +3802,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_10xmtx_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config b/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config index 7d4962ed..eb3ce2bc 100644 --- a/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_10xmtx_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_10xmtx_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts a 10x mtx into an h5mu file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml index 85448fd2..dde7e06e 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_bd_to_10x_molecular_barcode_tags" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -161,7 +161,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -179,11 +179,11 @@ build_info: output: "target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags" executable: "target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -213,7 +213,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf index 81c0435c..a3489640 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/main.nf @@ -1,4 +1,4 @@ -// from_bd_to_10x_molecular_barcode_tags v4.0.1 +// from_bd_to_10x_molecular_barcode_tags v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_bd_to_10x_molecular_barcode_tags", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3240,7 +3240,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3263,12 +3263,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3293,7 +3293,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3800,7 +3800,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_bd_to_10x_molecular_barcode_tags", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config index 58f4ac95..35bc0386 100644 --- a/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config +++ b/target/nextflow/convert/from_bd_to_10x_molecular_barcode_tags/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_bd_to_10x_molecular_barcode_tags' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert the molecular barcode sequence SAM tag from BD format (MA) to 10X format (UB).\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml index a8d39b54..70eba373 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_bdrhap_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -190,7 +190,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -219,11 +219,11 @@ build_info: output: "target/nextflow/convert/from_bdrhap_to_h5mu" executable: "target/nextflow/convert/from_bdrhap_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -253,7 +253,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf index d30a8ec3..200b2d3f 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_bdrhap_to_h5mu v4.0.1 +// from_bdrhap_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_bdrhap_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3288,7 +3288,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3324,12 +3324,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_bdrhap_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3354,7 +3354,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3839,7 +3839,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_bdrhap_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config b/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config index 05e7ac70..49c36461 100644 --- a/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_bdrhap_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_bdrhap_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert the output of a BD Rhapsody pipeline v2.x to a MuData h5 file.\n' author = 'Dorien Roosen, Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml index 5f67ddb3..af969470 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_cellranger_multi_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -245,11 +245,11 @@ build_info: output: "target/nextflow/convert/from_cellranger_multi_to_h5mu" executable: "target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -279,7 +279,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf index a002de9c..05015ffe 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_cellranger_multi_to_h5mu v4.0.1 +// from_cellranger_multi_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_cellranger_multi_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3304,7 +3304,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3352,12 +3352,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cellranger_multi_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3382,7 +3382,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3586,7 +3586,7 @@ def gather_input_data(dir: Path): found_input["count"] = dir feature_reference = found_input["count"] / "feature_reference.csv" - if feature_reference: + if feature_reference.is_file(): found_input["feature_reference"] = feature_reference per_sample_outs_dir = dir / "per_sample_outs" @@ -4279,7 +4279,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_cellranger_multi_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config b/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config index bbca3c37..f171f028 100644 --- a/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_cellranger_multi_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_cellranger_multi_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts the output from cellranger multi to a single .h5mu file.\nBy default, will map the following library type names to modality names:\n - Gene Expression: rna\n - Peaks: atac\n - Antibody Capture: prot\n - VDJ: vdj\n - VDJ-T: vdj_t\n - VDJ-B: vdj_b\n - CRISPR Guide Capture: crispr\n - Multiplexing Capture: hashing\n \nOther library types have their whitepace removed and dashes replaced by\nunderscores to generate the modality name.\n\nCurrently does not allow parsing the output from cell barcode demultiplexing.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml index 709f0e6c..1d2e13b4 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5ad_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5ad_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -173,7 +173,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -214,11 +214,11 @@ build_info: output: "target/nextflow/convert/from_h5ad_to_h5mu" executable: "target/nextflow/convert/from_h5ad_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -248,7 +248,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf index 4d3c86b6..7a75010c 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/main.nf +++ b/target/nextflow/convert/from_h5ad_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_h5ad_to_h5mu v4.0.1 +// from_h5ad_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_h5ad_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3253,7 +3253,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3309,12 +3309,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5ad_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3339,7 +3339,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3813,7 +3813,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_h5ad_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config b/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config index ed4269ac..00ba1603 100644 --- a/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_h5ad_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5ad_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts a single layer h5ad file into a single MuData object\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml index a6ff443f..7cb908b1 100644 --- a/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5ad_to_seurat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5ad_to_seurat" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -196,11 +196,11 @@ build_info: output: "target/nextflow/convert/from_h5ad_to_seurat" executable: "target/nextflow/convert/from_h5ad_to_seurat/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -230,7 +230,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_h5ad_to_seurat/main.nf b/target/nextflow/convert/from_h5ad_to_seurat/main.nf index 8a3ce97f..e38c59dd 100644 --- a/target/nextflow/convert/from_h5ad_to_seurat/main.nf +++ b/target/nextflow/convert/from_h5ad_to_seurat/main.nf @@ -1,4 +1,4 @@ -// from_h5ad_to_seurat v4.0.1 +// from_h5ad_to_seurat v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_h5ad_to_seurat", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3240,7 +3240,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3291,12 +3291,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5ad_to_seurat", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3321,7 +3321,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3783,7 +3783,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_h5ad_to_seurat", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config b/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config index ac9285dc..c51ed06f 100644 --- a/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config +++ b/target/nextflow/convert/from_h5ad_to_seurat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5ad_to_seurat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts an h5ad file into a Seurat file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml index 0abdc94b..4dbf1bd0 100644 --- a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_or_h5ad_to_seurat" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -166,7 +166,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -205,11 +205,11 @@ build_info: output: "target/nextflow/convert/from_h5mu_or_h5ad_to_seurat" executable: "target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -239,7 +239,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf index b7700999..361a69e1 100644 --- a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf +++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/main.nf @@ -1,4 +1,4 @@ -// from_h5mu_or_h5ad_to_seurat v4.0.1 +// from_h5mu_or_h5ad_to_seurat v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_h5mu_or_h5ad_to_seurat", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3246,7 +3246,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3299,12 +3299,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3329,7 +3329,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3853,7 +3853,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_h5mu_or_h5ad_to_seurat", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config index 3530c19a..9a844571 100644 --- a/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config +++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_seurat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5mu_or_h5ad_to_seurat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts an h5ad file or a single modality of an h5mu file into a Seurat file.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml index 66cb9815..416682ca 100644 --- a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_or_h5ad_to_tiledb" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -334,7 +334,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -381,11 +381,11 @@ build_info: output: "target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb" executable: "target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -415,7 +415,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf index b688d1de..b266f8c1 100644 --- a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf +++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/main.nf @@ -1,4 +1,4 @@ -// from_h5mu_or_h5ad_to_tiledb v4.0.1 +// from_h5mu_or_h5ad_to_tiledb v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_h5mu_or_h5ad_to_tiledb", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3438,7 +3438,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3503,12 +3503,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3533,7 +3533,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4666,7 +4666,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_h5mu_or_h5ad_to_tiledb", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config index 0e78c654..c474de70 100644 --- a/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config +++ b/target/nextflow/convert/from_h5mu_or_h5ad_to_tiledb/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5mu_or_h5ad_to_tiledb' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert a MuData or AnnData object to tiledb. Currently, transcriptome and protein modalities are supported.\n\nNOTE: The functionality provided by this component is experimental and may be subject to change. \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml index ccf37ce1..828dbdb3 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_h5ad/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_to_h5ad" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -174,7 +174,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -215,11 +215,11 @@ build_info: output: "target/nextflow/convert/from_h5mu_to_h5ad" executable: "target/nextflow/convert/from_h5mu_to_h5ad/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -249,7 +249,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf index 79b88792..96d89fa4 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/main.nf +++ b/target/nextflow/convert/from_h5mu_to_h5ad/main.nf @@ -1,4 +1,4 @@ -// from_h5mu_to_h5ad v4.0.1 +// from_h5mu_to_h5ad v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_h5mu_to_h5ad", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3259,7 +3259,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3315,12 +3315,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_h5ad", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3345,7 +3345,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3806,7 +3806,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_h5mu_to_h5ad", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config b/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config index 8c37f0c3..10767328 100644 --- a/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config +++ b/target/nextflow/convert/from_h5mu_to_h5ad/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5mu_to_h5ad' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts a h5mu file into a h5ad file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml index ca586cea..e5729792 100644 --- a/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_seurat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_h5mu_to_seurat" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -155,7 +155,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -188,11 +188,11 @@ build_info: output: "target/nextflow/convert/from_h5mu_to_seurat" executable: "target/nextflow/convert/from_h5mu_to_seurat/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -222,7 +222,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_h5mu_to_seurat/main.nf b/target/nextflow/convert/from_h5mu_to_seurat/main.nf index e35036c3..5d268ea3 100644 --- a/target/nextflow/convert/from_h5mu_to_seurat/main.nf +++ b/target/nextflow/convert/from_h5mu_to_seurat/main.nf @@ -1,4 +1,4 @@ -// from_h5mu_to_seurat v4.0.1 +// from_h5mu_to_seurat v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_h5mu_to_seurat", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3228,7 +3228,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3271,12 +3271,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_seurat", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3301,7 +3301,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3821,7 +3821,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_h5mu_to_seurat", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config b/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config index 211241c5..6d2b496d 100644 --- a/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config +++ b/target/nextflow/convert/from_h5mu_to_seurat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_h5mu_to_seurat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts an h5mu file into a Seurat file.\n\nRestrictions:\n - Only the intersection of cells is currently loaded into the Seurat object due to the object structure limitation.\n - Multimodal embeddings (global .obsm slot) are loaded with the assay.used field set to the default assay.\n - Embeddings names are changed in order to comply with R & Seurat requirements and conventions.\n - Feature names with underscores (\'_\') are automatically replaced with dashes (\'-\')\n - Seurat does not support global variables metadata /var.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml index 92659130..7a619b34 100644 --- a/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_seurat_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_seurat_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -312,7 +312,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -388,11 +388,11 @@ build_info: output: "target/nextflow/convert/from_seurat_to_h5mu" executable: "target/nextflow/convert/from_seurat_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -422,7 +422,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_seurat_to_h5mu/main.nf b/target/nextflow/convert/from_seurat_to_h5mu/main.nf index 13ccc978..59994652 100644 --- a/target/nextflow/convert/from_seurat_to_h5mu/main.nf +++ b/target/nextflow/convert/from_seurat_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_seurat_to_h5mu v4.0.1 +// from_seurat_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_seurat_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3401,7 +3401,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3505,12 +3505,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_seurat_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3535,7 +3535,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4062,7 +4062,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_seurat_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config b/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config index eb40fee6..368afea6 100644 --- a/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_seurat_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_seurat_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Converts a Seurat file into an H5MU file.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml index a5daacad..948a43d7 100644 --- a/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_tiledb_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "from_tiledb_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -214,7 +214,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -258,11 +258,11 @@ build_info: output: "target/nextflow/convert/from_tiledb_to_h5mu" executable: "target/nextflow/convert/from_tiledb_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/from_tiledb_to_h5mu/main.nf b/target/nextflow/convert/from_tiledb_to_h5mu/main.nf index a490c6b0..dc663e8f 100644 --- a/target/nextflow/convert/from_tiledb_to_h5mu/main.nf +++ b/target/nextflow/convert/from_tiledb_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// from_tiledb_to_h5mu v4.0.1 +// from_tiledb_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "from_tiledb_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3303,7 +3303,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3362,12 +3362,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_tiledb_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3392,7 +3392,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3935,7 +3935,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/from_tiledb_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config b/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config index 720dac4b..7c2e77cb 100644 --- a/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config +++ b/target/nextflow/convert/from_tiledb_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/from_tiledb_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' author = 'Dries Schaumont' } diff --git a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml index b37be983..55229202 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/velocyto_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "velocyto_to_h5mu" namespace: "convert" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -244,7 +244,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -275,11 +275,11 @@ build_info: output: "target/nextflow/convert/velocyto_to_h5mu" executable: "target/nextflow/convert/velocyto_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -309,7 +309,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/convert/velocyto_to_h5mu/main.nf b/target/nextflow/convert/velocyto_to_h5mu/main.nf index 04f0b6a5..4b901707 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/main.nf +++ b/target/nextflow/convert/velocyto_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// velocyto_to_h5mu v4.0.1 +// velocyto_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "velocyto_to_h5mu", "namespace" : "convert", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3355,7 +3355,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3393,12 +3393,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/velocyto_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3423,7 +3423,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3913,7 +3913,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/convert/velocyto_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/convert/velocyto_to_h5mu/nextflow.config b/target/nextflow/convert/velocyto_to_h5mu/nextflow.config index 7a2c7f4f..dd3f35ec 100644 --- a/target/nextflow/convert/velocyto_to_h5mu/nextflow.config +++ b/target/nextflow/convert/velocyto_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'convert/velocyto_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert a velocyto loom file to a h5mu file.\n\nIf an input h5mu file is also provided, the velocity\nh5ad object will get added to that h5mu instead.\n' author = 'Dries Schaumont, Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml index 279ac1c7..09682d3a 100644 --- a/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml +++ b/target/nextflow/correction/cellbender_remove_background/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellbender_remove_background" namespace: "correction" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Inputs" arguments: @@ -578,7 +578,7 @@ engines: id: "docker" image: "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -611,11 +611,11 @@ build_info: output: "target/nextflow/correction/cellbender_remove_background" executable: "target/nextflow/correction/cellbender_remove_background/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -645,7 +645,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/correction/cellbender_remove_background/main.nf b/target/nextflow/correction/cellbender_remove_background/main.nf index 0bb0d4b4..77f1b494 100644 --- a/target/nextflow/correction/cellbender_remove_background/main.nf +++ b/target/nextflow/correction/cellbender_remove_background/main.nf @@ -1,4 +1,4 @@ -// cellbender_remove_background v4.0.1 +// cellbender_remove_background v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellbender_remove_background", "namespace" : "correction", - "version" : "v4.0.1", + "version" : "v4.0.2", "argument_groups" : [ { "name" : "Inputs", @@ -3659,7 +3659,7 @@ meta = [ "id" : "docker", "image" : "nvcr.io/nvidia/cuda:11.8.0-devel-ubuntu22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3696,12 +3696,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/correction/cellbender_remove_background", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3726,7 +3726,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4404,7 +4404,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/correction/cellbender_remove_background", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midcpu", diff --git a/target/nextflow/correction/cellbender_remove_background/nextflow.config b/target/nextflow/correction/cellbender_remove_background/nextflow.config index 6300b267..ad55b6bb 100644 --- a/target/nextflow/correction/cellbender_remove_background/nextflow.config +++ b/target/nextflow/correction/cellbender_remove_background/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'correction/cellbender_remove_background' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Eliminating technical artifacts from high-throughput single-cell RNA sequencing data.\n\nThis module removes counts due to ambient RNA molecules and random barcode swapping from (raw) UMI-based scRNA-seq count matrices. \nAt the moment, only the count matrices produced by the CellRanger count pipeline is supported. Support for additional tools and protocols \nwill be added in the future. A quick start tutorial can be found here.\n\nFleming et al. 2022, bioRxiv.\n' } diff --git a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml index 99df40db..05228f22 100644 --- a/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml +++ b/target/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "concatenate_h5mu" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -253,7 +253,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -300,11 +300,11 @@ build_info: output: "target/nextflow/dataflow/concatenate_h5mu" executable: "target/nextflow/dataflow/concatenate_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -334,7 +334,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dataflow/concatenate_h5mu/main.nf b/target/nextflow/dataflow/concatenate_h5mu/main.nf index f32e613f..c12b5cd7 100644 --- a/target/nextflow/dataflow/concatenate_h5mu/main.nf +++ b/target/nextflow/dataflow/concatenate_h5mu/main.nf @@ -1,4 +1,4 @@ -// concatenate_h5mu v4.0.1 +// concatenate_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "concatenate_h5mu", "namespace" : "dataflow", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3328,7 +3328,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3393,12 +3393,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dataflow/concatenate_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3423,7 +3423,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4266,7 +4266,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dataflow/concatenate_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midcpu", diff --git a/target/nextflow/dataflow/concatenate_h5mu/nextflow.config b/target/nextflow/dataflow/concatenate_h5mu/nextflow.config index b8b3566b..c716b1f8 100644 --- a/target/nextflow/dataflow/concatenate_h5mu/nextflow.config +++ b/target/nextflow/dataflow/concatenate_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/concatenate_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/dataflow/merge/.config.vsh.yaml b/target/nextflow/dataflow/merge/.config.vsh.yaml index 200bb1ba..0cfdabba 100644 --- a/target/nextflow/dataflow/merge/.config.vsh.yaml +++ b/target/nextflow/dataflow/merge/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "merge" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -163,7 +163,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -204,11 +204,11 @@ build_info: output: "target/nextflow/dataflow/merge" executable: "target/nextflow/dataflow/merge/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -238,7 +238,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dataflow/merge/main.nf b/target/nextflow/dataflow/merge/main.nf index 98655694..fe4ec0a5 100644 --- a/target/nextflow/dataflow/merge/main.nf +++ b/target/nextflow/dataflow/merge/main.nf @@ -1,4 +1,4 @@ -// merge v4.0.1 +// merge v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "merge", "namespace" : "dataflow", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3246,7 +3246,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3302,12 +3302,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dataflow/merge", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3332,7 +3332,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3847,7 +3847,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dataflow/merge", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/dataflow/merge/nextflow.config b/target/nextflow/dataflow/merge/nextflow.config index c57d0781..f4d9aeca 100644 --- a/target/nextflow/dataflow/merge/nextflow.config +++ b/target/nextflow/dataflow/merge/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/merge' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Combine one or more single-modality .h5mu files together into one .h5mu file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml b/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml index 55e6f3fe..c4c2d0a8 100644 --- a/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml +++ b/target/nextflow/dataflow/split_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_h5mu" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -203,7 +203,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -244,11 +244,11 @@ build_info: output: "target/nextflow/dataflow/split_h5mu" executable: "target/nextflow/dataflow/split_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -278,7 +278,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dataflow/split_h5mu/main.nf b/target/nextflow/dataflow/split_h5mu/main.nf index c31ca576..8737269c 100644 --- a/target/nextflow/dataflow/split_h5mu/main.nf +++ b/target/nextflow/dataflow/split_h5mu/main.nf @@ -1,4 +1,4 @@ -// split_h5mu v4.0.1 +// split_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "split_h5mu", "namespace" : "dataflow", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3285,7 +3285,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3341,12 +3341,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dataflow/split_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3371,7 +3371,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3908,7 +3908,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dataflow/split_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/dataflow/split_h5mu/nextflow.config b/target/nextflow/dataflow/split_h5mu/nextflow.config index d60d18b8..06731191 100644 --- a/target/nextflow/dataflow/split_h5mu/nextflow.config +++ b/target/nextflow/dataflow/split_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/split_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Split the samples of a single modality from a .h5mu (multimodal) sample into seperate .h5mu files based on the values of an .obs column of this modality. \n' author = 'Dorien Roosen' } diff --git a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml index 55701c3f..7b551c7b 100644 --- a/target/nextflow/dataflow/split_modalities/.config.vsh.yaml +++ b/target/nextflow/dataflow/split_modalities/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "split_modalities" namespace: "dataflow" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -190,7 +190,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -231,11 +231,11 @@ build_info: output: "target/nextflow/dataflow/split_modalities" executable: "target/nextflow/dataflow/split_modalities/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -265,7 +265,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dataflow/split_modalities/main.nf b/target/nextflow/dataflow/split_modalities/main.nf index ebda9586..0fb40234 100644 --- a/target/nextflow/dataflow/split_modalities/main.nf +++ b/target/nextflow/dataflow/split_modalities/main.nf @@ -1,4 +1,4 @@ -// split_modalities v4.0.1 +// split_modalities v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "split_modalities", "namespace" : "dataflow", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3280,7 +3280,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3336,12 +3336,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dataflow/split_modalities", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3366,7 +3366,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3865,7 +3865,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dataflow/split_modalities", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/dataflow/split_modalities/nextflow.config b/target/nextflow/dataflow/split_modalities/nextflow.config index 11770fe7..49fb3fb4 100644 --- a/target/nextflow/dataflow/split_modalities/nextflow.config +++ b/target/nextflow/dataflow/split_modalities/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/split_modalities' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Split the modalities from a single .h5mu multimodal sample into seperate .h5mu files. \n' author = 'Dries Schaumont, Robrecht Cannoodt' } diff --git a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml index b38b3f75..a0e9fc57 100644 --- a/target/nextflow/demux/bcl2fastq/.config.vsh.yaml +++ b/target/nextflow/demux/bcl2fastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcl2fastq" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Toni Verbeiren" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/bcl2fastq:2.20" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -196,11 +196,11 @@ build_info: output: "target/nextflow/demux/bcl2fastq" executable: "target/nextflow/demux/bcl2fastq/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -230,7 +230,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/demux/bcl2fastq/main.nf b/target/nextflow/demux/bcl2fastq/main.nf index 8c2578de..b2c2d3f8 100644 --- a/target/nextflow/demux/bcl2fastq/main.nf +++ b/target/nextflow/demux/bcl2fastq/main.nf @@ -1,4 +1,4 @@ -// bcl2fastq v4.0.1 +// bcl2fastq v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bcl2fastq", "namespace" : "demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -3259,7 +3259,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/bcl2fastq:2.20", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3282,12 +3282,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/demux/bcl2fastq", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3312,7 +3312,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3771,7 +3771,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/demux/bcl2fastq", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/demux/bcl2fastq/nextflow.config b/target/nextflow/demux/bcl2fastq/nextflow.config index ec6b8843..f9c67501 100644 --- a/target/nextflow/demux/bcl2fastq/nextflow.config +++ b/target/nextflow/demux/bcl2fastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/bcl2fastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert bcl files to fastq files using bcl2fastq.\n' author = 'Toni Verbeiren' } diff --git a/target/nextflow/demux/bcl_convert/.config.vsh.yaml b/target/nextflow/demux/bcl_convert/.config.vsh.yaml index 15830b17..0d74db24 100644 --- a/target/nextflow/demux/bcl_convert/.config.vsh.yaml +++ b/target/nextflow/demux/bcl_convert/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcl_convert" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Toni Verbeiren" roles: @@ -250,7 +250,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/bclconvert:4.2" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -268,11 +268,11 @@ build_info: output: "target/nextflow/demux/bcl_convert" executable: "target/nextflow/demux/bcl_convert/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -302,7 +302,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/demux/bcl_convert/main.nf b/target/nextflow/demux/bcl_convert/main.nf index 97eac16a..bf8fcec4 100644 --- a/target/nextflow/demux/bcl_convert/main.nf +++ b/target/nextflow/demux/bcl_convert/main.nf @@ -1,4 +1,4 @@ -// bcl_convert v4.0.1 +// bcl_convert v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3038,7 +3038,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bcl_convert", "namespace" : "demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -3363,7 +3363,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/bclconvert:4.2", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3386,12 +3386,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/demux/bcl_convert", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3416,7 +3416,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3882,7 +3882,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/demux/bcl_convert", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/demux/bcl_convert/nextflow.config b/target/nextflow/demux/bcl_convert/nextflow.config index ec032a1f..f36d9440 100644 --- a/target/nextflow/demux/bcl_convert/nextflow.config +++ b/target/nextflow/demux/bcl_convert/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/bcl_convert' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\nhttps://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html\nand https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html\n' author = 'Toni Verbeiren, Marijke Van Moerbeke, Weiwei Schultz, Dorien Roosen' } diff --git a/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml b/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml index cd87966f..4615b1f7 100644 --- a/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml +++ b/target/nextflow/demux/cellranger_atac_mkfastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_atac_mkfastq" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -213,7 +213,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger_atac:2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -237,11 +237,11 @@ build_info: output: "target/nextflow/demux/cellranger_atac_mkfastq" executable: "target/nextflow/demux/cellranger_atac_mkfastq/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -271,7 +271,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/demux/cellranger_atac_mkfastq/main.nf b/target/nextflow/demux/cellranger_atac_mkfastq/main.nf index 7855c9ba..4c914af7 100644 --- a/target/nextflow/demux/cellranger_atac_mkfastq/main.nf +++ b/target/nextflow/demux/cellranger_atac_mkfastq/main.nf @@ -1,4 +1,4 @@ -// cellranger_atac_mkfastq v4.0.1 +// cellranger_atac_mkfastq v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_atac_mkfastq", "namespace" : "demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3295,7 +3295,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger_atac:2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3327,12 +3327,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/demux/cellranger_atac_mkfastq", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3357,7 +3357,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3852,7 +3852,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/demux/cellranger_atac_mkfastq", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config b/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config index bb6fca46..9886de77 100644 --- a/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config +++ b/target/nextflow/demux/cellranger_atac_mkfastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/cellranger_atac_mkfastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Demultiplex raw sequencing data for ATAC experiments' author = 'Vladimir Shitov' } diff --git a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml index e9fdc238..76bb7d27 100644 --- a/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml +++ b/target/nextflow/demux/cellranger_mkfastq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mkfastq" namespace: "demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -204,7 +204,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -228,11 +228,11 @@ build_info: output: "target/nextflow/demux/cellranger_mkfastq" executable: "target/nextflow/demux/cellranger_mkfastq/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -262,7 +262,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/demux/cellranger_mkfastq/main.nf b/target/nextflow/demux/cellranger_mkfastq/main.nf index c2d5fff8..aba4fd11 100644 --- a/target/nextflow/demux/cellranger_mkfastq/main.nf +++ b/target/nextflow/demux/cellranger_mkfastq/main.nf @@ -1,4 +1,4 @@ -// cellranger_mkfastq v4.0.1 +// cellranger_mkfastq v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_mkfastq", "namespace" : "demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3306,7 +3306,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger:9.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3338,12 +3338,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/demux/cellranger_mkfastq", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3368,7 +3368,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3859,7 +3859,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/demux/cellranger_mkfastq", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/demux/cellranger_mkfastq/nextflow.config b/target/nextflow/demux/cellranger_mkfastq/nextflow.config index 8f7ec5be..4b6250de 100644 --- a/target/nextflow/demux/cellranger_mkfastq/nextflow.config +++ b/target/nextflow/demux/cellranger_mkfastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demux/cellranger_mkfastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Demultiplex raw sequencing data' author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml b/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml index 7bf8bd54..8816e8be 100644 --- a/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml +++ b/target/nextflow/differential_expression/create_pseudobulk/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pseudobulk" namespace: "differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -271,7 +271,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -309,11 +309,11 @@ build_info: output: "target/nextflow/differential_expression/create_pseudobulk" executable: "target/nextflow/differential_expression/create_pseudobulk/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -343,7 +343,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/differential_expression/create_pseudobulk/main.nf b/target/nextflow/differential_expression/create_pseudobulk/main.nf index 6b6912f2..97a56838 100644 --- a/target/nextflow/differential_expression/create_pseudobulk/main.nf +++ b/target/nextflow/differential_expression/create_pseudobulk/main.nf @@ -1,4 +1,4 @@ -// create_pseudobulk v4.0.1 +// create_pseudobulk v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3038,7 +3038,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_pseudobulk", "namespace" : "differential_expression", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3386,7 +3386,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3436,12 +3436,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/differential_expression/create_pseudobulk", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3466,7 +3466,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3996,7 +3996,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/differential_expression/create_pseudobulk", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/differential_expression/create_pseudobulk/nextflow.config b/target/nextflow/differential_expression/create_pseudobulk/nextflow.config index 45bb5115..e7c19424 100644 --- a/target/nextflow/differential_expression/create_pseudobulk/nextflow.config +++ b/target/nextflow/differential_expression/create_pseudobulk/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'differential_expression/create_pseudobulk' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Generation of pseudobulk samples from single-cell transcriptomics data,\nby aggregating raw gene expression counts from individual cells to create \nbulk-like expression profiles suitable for differential expression analysis\nwith methods designed for bulk differential expression analysis.\nNote that this componentonly considers factors as explanatory variables, \nand excludes covariates from the analysis.\n' author = 'Dorien Roosen, Jakub Majercik, Dries De Maeyer, Weiwei Schultz' } diff --git a/target/nextflow/differential_expression/deseq2/.config.vsh.yaml b/target/nextflow/differential_expression/deseq2/.config.vsh.yaml index cb340b35..cb92cafa 100644 --- a/target/nextflow/differential_expression/deseq2/.config.vsh.yaml +++ b/target/nextflow/differential_expression/deseq2/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "deseq2" namespace: "differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -294,7 +294,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -346,11 +346,11 @@ build_info: output: "target/nextflow/differential_expression/deseq2" executable: "target/nextflow/differential_expression/deseq2/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -380,7 +380,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/differential_expression/deseq2/main.nf b/target/nextflow/differential_expression/deseq2/main.nf index 3caf80e6..5942467f 100644 --- a/target/nextflow/differential_expression/deseq2/main.nf +++ b/target/nextflow/differential_expression/deseq2/main.nf @@ -1,4 +1,4 @@ -// deseq2 v4.0.1 +// deseq2 v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3038,7 +3038,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "deseq2", "namespace" : "differential_expression", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3399,7 +3399,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3475,12 +3475,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/differential_expression/deseq2", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3505,7 +3505,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4350,7 +4350,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/differential_expression/deseq2", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/differential_expression/deseq2/nextflow.config b/target/nextflow/differential_expression/deseq2/nextflow.config index 15d54314..132c922a 100644 --- a/target/nextflow/differential_expression/deseq2/nextflow.config +++ b/target/nextflow/differential_expression/deseq2/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'differential_expression/deseq2' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs differential expression analysis using DESeq2 on bulk samples or pseudobulk samples aggregated from single-cell data.\nNote that this component only considers factors as explanatory variables, and excludes covariates from the analysis.\n' author = 'Jakub Majercik, Dorien Roosen, Dries De Maeyer, Weiwei Schultz' } diff --git a/target/nextflow/dimred/densmap/.config.vsh.yaml b/target/nextflow/dimred/densmap/.config.vsh.yaml index 5d005f57..6935dcf0 100644 --- a/target/nextflow/dimred/densmap/.config.vsh.yaml +++ b/target/nextflow/dimred/densmap/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "densmap" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -353,7 +353,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -395,11 +395,11 @@ build_info: output: "target/nextflow/dimred/densmap" executable: "target/nextflow/dimred/densmap/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -429,7 +429,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dimred/densmap/main.nf b/target/nextflow/dimred/densmap/main.nf index b3d700b1..d320f601 100644 --- a/target/nextflow/dimred/densmap/main.nf +++ b/target/nextflow/dimred/densmap/main.nf @@ -1,4 +1,4 @@ -// densmap v4.0.1 +// densmap v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "densmap", "namespace" : "dimred", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3449,7 +3449,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3506,12 +3506,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dimred/densmap", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3536,7 +3536,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4076,7 +4076,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dimred/densmap", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/dimred/densmap/nextflow.config b/target/nextflow/dimred/densmap/nextflow.config index 249ef102..6f65c000 100644 --- a/target/nextflow/dimred/densmap/nextflow.config +++ b/target/nextflow/dimred/densmap/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/densmap' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A modification of UMAP that adds an extra cost term in order to preserve information \nabout the relative local density of the data. It is performed on the same inputs as UMAP.\n' author = 'Jakub Majercik' } diff --git a/target/nextflow/dimred/lsi/.config.vsh.yaml b/target/nextflow/dimred/lsi/.config.vsh.yaml index 374f189c..059733c5 100644 --- a/target/nextflow/dimred/lsi/.config.vsh.yaml +++ b/target/nextflow/dimred/lsi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lsi" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Sarah Ouologuem" roles: @@ -269,7 +269,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -314,11 +314,11 @@ build_info: output: "target/nextflow/dimred/lsi" executable: "target/nextflow/dimred/lsi/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -348,7 +348,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dimred/lsi/main.nf b/target/nextflow/dimred/lsi/main.nf index 84189277..53537321 100644 --- a/target/nextflow/dimred/lsi/main.nf +++ b/target/nextflow/dimred/lsi/main.nf @@ -1,4 +1,4 @@ -// lsi v4.0.1 +// lsi v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "lsi", "namespace" : "dimred", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Sarah Ouologuem", @@ -3383,7 +3383,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3443,12 +3443,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dimred/lsi", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3473,7 +3473,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4023,7 +4023,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dimred/lsi", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/dimred/lsi/nextflow.config b/target/nextflow/dimred/lsi/nextflow.config index f3a6597e..17b1b028 100644 --- a/target/nextflow/dimred/lsi/nextflow.config +++ b/target/nextflow/dimred/lsi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/lsi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy.\n' author = 'Sarah Ouologuem, Vladimir Shitov' } diff --git a/target/nextflow/dimred/pca/.config.vsh.yaml b/target/nextflow/dimred/pca/.config.vsh.yaml index 99356f04..da49ee66 100644 --- a/target/nextflow/dimred/pca/.config.vsh.yaml +++ b/target/nextflow/dimred/pca/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pca" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -240,7 +240,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -276,11 +276,11 @@ build_info: output: "target/nextflow/dimred/pca" executable: "target/nextflow/dimred/pca/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -310,7 +310,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dimred/pca/main.nf b/target/nextflow/dimred/pca/main.nf index 74ddbccc..673a4972 100644 --- a/target/nextflow/dimred/pca/main.nf +++ b/target/nextflow/dimred/pca/main.nf @@ -1,4 +1,4 @@ -// pca v4.0.1 +// pca v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "pca", "namespace" : "dimred", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3333,7 +3333,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3380,12 +3380,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dimred/pca", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3410,7 +3410,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3933,7 +3933,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dimred/pca", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/dimred/pca/nextflow.config b/target/nextflow/dimred/pca/nextflow.config index 87744c8c..40180993 100644 --- a/target/nextflow/dimred/pca/nextflow.config +++ b/target/nextflow/dimred/pca/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/pca' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Computes PCA coordinates, loadings and variance decomposition. Uses the implementation of scikit-learn [Pedregosa11].\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/dimred/tsne/.config.vsh.yaml b/target/nextflow/dimred/tsne/.config.vsh.yaml index 9c4cfdd9..23bc0389 100644 --- a/target/nextflow/dimred/tsne/.config.vsh.yaml +++ b/target/nextflow/dimred/tsne/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tsne" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -281,7 +281,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -323,11 +323,11 @@ build_info: output: "target/nextflow/dimred/tsne" executable: "target/nextflow/dimred/tsne/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -357,7 +357,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dimred/tsne/main.nf b/target/nextflow/dimred/tsne/main.nf index eb62110e..0c911775 100644 --- a/target/nextflow/dimred/tsne/main.nf +++ b/target/nextflow/dimred/tsne/main.nf @@ -1,4 +1,4 @@ -// tsne v4.0.1 +// tsne v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "tsne", "namespace" : "dimred", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3373,7 +3373,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3430,12 +3430,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dimred/tsne", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3460,7 +3460,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3964,7 +3964,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dimred/tsne", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/dimred/tsne/nextflow.config b/target/nextflow/dimred/tsne/nextflow.config index 97421139..56e1c27d 100644 --- a/target/nextflow/dimred/tsne/nextflow.config +++ b/target/nextflow/dimred/tsne/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/tsne' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 't-SNE (t-Distributed Stochastic Neighbor Embedding) is a dimensionality reduction technique used to visualize high-dimensional data in a low-dimensional space, revealing patterns and clusters by preserving local data similarities.\n' author = 'Jakub Majercik' } diff --git a/target/nextflow/dimred/umap/.config.vsh.yaml b/target/nextflow/dimred/umap/.config.vsh.yaml index 7bf49dab..fb378b99 100644 --- a/target/nextflow/dimred/umap/.config.vsh.yaml +++ b/target/nextflow/dimred/umap/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umap" namespace: "dimred" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -294,7 +294,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -330,11 +330,11 @@ build_info: output: "target/nextflow/dimred/umap" executable: "target/nextflow/dimred/umap/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -364,7 +364,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/dimred/umap/main.nf b/target/nextflow/dimred/umap/main.nf index fc795e69..02a69403 100644 --- a/target/nextflow/dimred/umap/main.nf +++ b/target/nextflow/dimred/umap/main.nf @@ -1,4 +1,4 @@ -// umap v4.0.1 +// umap v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umap", "namespace" : "dimred", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3382,7 +3382,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3429,12 +3429,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dimred/umap", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3459,7 +3459,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3971,7 +3971,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/dimred/umap", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/dimred/umap/nextflow.config b/target/nextflow/dimred/umap/nextflow.config index 67b7637f..bc69bab7 100644 --- a/target/nextflow/dimred/umap/nextflow.config +++ b/target/nextflow/dimred/umap/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dimred/umap' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'UMAP (Uniform Manifold Approximation and Projection) is a manifold learning technique suitable for visualizing high-dimensional data. Besides tending to be faster than tSNE, it optimizes the embedding such that it best reflects the topology of the data, which we represent throughout Scanpy using a neighborhood graph. tSNE, by contrast, optimizes the distribution of nearest-neighbor distances in the embedding such that these best match the distribution of distances in the high-dimensional space. We use the implementation of umap-learn [McInnes18]. For a few comparisons of UMAP with tSNE, see this preprint.\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/download/download_file/.config.vsh.yaml b/target/nextflow/download/download_file/.config.vsh.yaml index b1aa7101..34f03b81 100644 --- a/target/nextflow/download/download_file/.config.vsh.yaml +++ b/target/nextflow/download/download_file/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "download_file" namespace: "download" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -146,7 +146,7 @@ engines: id: "docker" image: "bash:5.1.16" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -159,11 +159,11 @@ build_info: output: "target/nextflow/download/download_file" executable: "target/nextflow/download/download_file/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -193,7 +193,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/download/download_file/main.nf b/target/nextflow/download/download_file/main.nf index e985e081..d408867b 100644 --- a/target/nextflow/download/download_file/main.nf +++ b/target/nextflow/download/download_file/main.nf @@ -1,4 +1,4 @@ -// download_file v4.0.1 +// download_file v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "download_file", "namespace" : "download", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3221,7 +3221,7 @@ meta = [ "id" : "docker", "image" : "bash:5.1.16", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/" }, { @@ -3235,12 +3235,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/download/download_file", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3265,7 +3265,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3712,7 +3712,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/download/download_file", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/download/download_file/nextflow.config b/target/nextflow/download/download_file/nextflow.config index 282abd60..847d32b6 100644 --- a/target/nextflow/download/download_file/nextflow.config +++ b/target/nextflow/download/download_file/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'download/download_file' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Download a file.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml b/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml index cd539778..7603f9ac 100644 --- a/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml +++ b/target/nextflow/feature_annotation/align_query_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "align_query_reference" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -476,7 +476,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -517,11 +517,11 @@ build_info: output: "target/nextflow/feature_annotation/align_query_reference" executable: "target/nextflow/feature_annotation/align_query_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -551,7 +551,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/feature_annotation/align_query_reference/main.nf b/target/nextflow/feature_annotation/align_query_reference/main.nf index 01a9aac4..a4405550 100644 --- a/target/nextflow/feature_annotation/align_query_reference/main.nf +++ b/target/nextflow/feature_annotation/align_query_reference/main.nf @@ -1,4 +1,4 @@ -// align_query_reference v4.0.1 +// align_query_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "align_query_reference", "namespace" : "feature_annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3583,7 +3583,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3639,12 +3639,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/feature_annotation/align_query_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3669,7 +3669,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4399,7 +4399,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/feature_annotation/align_query_reference", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/feature_annotation/align_query_reference/nextflow.config b/target/nextflow/feature_annotation/align_query_reference/nextflow.config index d27bb3cf..81e6f26d 100644 --- a/target/nextflow/feature_annotation/align_query_reference/nextflow.config +++ b/target/nextflow/feature_annotation/align_query_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'feature_annotation/align_query_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Alignment of a query and reference dataset by:\n* Alignment of layers\n* Harmonization of .obs field names for batch and cell type labels\n* Harmonization of .var field name for gene names\n* Sanitation of gene names\n* Cross-checking of genes\n* Assignment of an id to the query and reference datasets\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml index 0049ddb5..6985259c 100644 --- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml +++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "highly_variable_features_scanpy" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -342,7 +342,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -381,11 +381,11 @@ build_info: output: "target/nextflow/feature_annotation/highly_variable_features_scanpy" executable: "target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -415,7 +415,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf b/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf index 53c6419a..e196e46d 100644 --- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf +++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf @@ -1,4 +1,4 @@ -// highly_variable_features_scanpy v4.0.1 +// highly_variable_features_scanpy v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "highly_variable_features_scanpy", "namespace" : "feature_annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3430,7 +3430,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3481,12 +3481,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/feature_annotation/highly_variable_features_scanpy", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3511,7 +3511,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4110,7 +4110,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/feature_annotation/highly_variable_features_scanpy", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config b/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config index d5696168..7195163d 100644 --- a/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config +++ b/target/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'feature_annotation/highly_variable_features_scanpy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Annotate highly variable features [Satija15] [Zheng17] [Stuart19].\n\nExpects logarithmized data, except when flavor=\'seurat_v3\' in which count data is expected.\n\nDepending on flavor, this reproduces the R-implementations of Seurat [Satija15], Cell Ranger [Zheng17], and Seurat v3 [Stuart19].\n\nFor the dispersion-based methods ([Satija15] and [Zheng17]), the normalized dispersion is obtained by scaling with the mean and standard deviation of the dispersions for features falling into a given bin for mean expression of features. This means that for each bin of mean expression, highly variable features are selected.\n\nFor [Stuart19], a normalized variance for each feature is computed. First, the data are standardized (i.e., z-score normalization per feature) with a regularized standard deviation. Next, the normalized variance is computed as the variance of each feature after the transformation. Features are ranked by the normalized variance.\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml index d61a317d..1ace1c8b 100644 --- a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml +++ b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "score_genes_cell_cycle_scanpy" namespace: "feature_annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -367,7 +367,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -399,11 +399,11 @@ build_info: output: "target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy" executable: "target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -433,7 +433,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf index 8cca1119..f5ad5edd 100644 --- a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf +++ b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf @@ -1,4 +1,4 @@ -// score_genes_cell_cycle_scanpy v4.0.1 +// score_genes_cell_cycle_scanpy v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "score_genes_cell_cycle_scanpy", "namespace" : "feature_annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3484,7 +3484,7 @@ meta = [ "id" : "docker", "image" : "python:3.11", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3524,12 +3524,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3554,7 +3554,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4085,7 +4085,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/feature_annotation/score_genes_cell_cycle_scanpy", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config index f378e5e1..6e0f0c7c 100644 --- a/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config +++ b/target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'feature_annotation/score_genes_cell_cycle_scanpy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Calculates the score associated to S phase and G2M phase and annotates the cell cycle phase for each cell, as implemented by scanpy. \nThe score is the average expression of a set of genes subtracted with the average expression of a reference set of genes.\n' author = 'Robrecht Cannoodt, Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/files/make_params/.config.vsh.yaml b/target/nextflow/files/make_params/.config.vsh.yaml index 64a5a0f8..4b90c505 100644 --- a/target/nextflow/files/make_params/.config.vsh.yaml +++ b/target/nextflow/files/make_params/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "make_params" namespace: "files" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -223,7 +223,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/randpy:r4.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -236,11 +236,11 @@ build_info: output: "target/nextflow/files/make_params" executable: "target/nextflow/files/make_params/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -270,7 +270,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/files/make_params/main.nf b/target/nextflow/files/make_params/main.nf index 40b455a9..b7d5a780 100644 --- a/target/nextflow/files/make_params/main.nf +++ b/target/nextflow/files/make_params/main.nf @@ -1,4 +1,4 @@ -// make_params v4.0.1 +// make_params v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "make_params", "namespace" : "files", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3321,7 +3321,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/randpy:r4.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/" }, { @@ -3335,12 +3335,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/files/make_params", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3365,7 +3365,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3881,7 +3881,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/files/make_params", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/files/make_params/nextflow.config b/target/nextflow/files/make_params/nextflow.config index 17400274..06df3998 100644 --- a/target/nextflow/files/make_params/nextflow.config +++ b/target/nextflow/files/make_params/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'files/make_params' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Looks for files in a directory and turn it in a params file.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml index 1b073fa5..1f2d5f98 100644 --- a/target/nextflow/filter/delimit_fraction/.config.vsh.yaml +++ b/target/nextflow/filter/delimit_fraction/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "delimit_fraction" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -219,7 +219,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -260,11 +260,11 @@ build_info: output: "target/nextflow/filter/delimit_fraction" executable: "target/nextflow/filter/delimit_fraction/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -294,7 +294,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/delimit_fraction/main.nf b/target/nextflow/filter/delimit_fraction/main.nf index 3ce02f81..cd485058 100644 --- a/target/nextflow/filter/delimit_fraction/main.nf +++ b/target/nextflow/filter/delimit_fraction/main.nf @@ -1,4 +1,4 @@ -// delimit_fraction v4.0.1 +// delimit_fraction v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "delimit_fraction", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3312,7 +3312,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3368,12 +3368,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/delimit_fraction", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3398,7 +3398,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3928,7 +3928,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/delimit_fraction", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/filter/delimit_fraction/nextflow.config b/target/nextflow/filter/delimit_fraction/nextflow.config index 973dd925..940bbaee 100644 --- a/target/nextflow/filter/delimit_fraction/nextflow.config +++ b/target/nextflow/filter/delimit_fraction/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/delimit_fraction' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Turns a column containing values between 0 and 1 into a boolean column based on thresholds.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/filter/do_filter/.config.vsh.yaml b/target/nextflow/filter/do_filter/.config.vsh.yaml index bf2bf738..c87bbf7d 100644 --- a/target/nextflow/filter/do_filter/.config.vsh.yaml +++ b/target/nextflow/filter/do_filter/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "do_filter" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -193,7 +193,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -228,11 +228,11 @@ build_info: output: "target/nextflow/filter/do_filter" executable: "target/nextflow/filter/do_filter/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -262,7 +262,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/do_filter/main.nf b/target/nextflow/filter/do_filter/main.nf index 2f4a45f8..6edcbde3 100644 --- a/target/nextflow/filter/do_filter/main.nf +++ b/target/nextflow/filter/do_filter/main.nf @@ -1,4 +1,4 @@ -// do_filter v4.0.1 +// do_filter v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "do_filter", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3282,7 +3282,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3328,12 +3328,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/do_filter", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3358,7 +3358,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3851,7 +3851,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/do_filter", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/filter/do_filter/nextflow.config b/target/nextflow/filter/do_filter/nextflow.config index cea4cbbb..461bcba0 100644 --- a/target/nextflow/filter/do_filter/nextflow.config +++ b/target/nextflow/filter/do_filter/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/do_filter' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Remove observations and variables based on specified .obs and .var columns.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml index 9b46a06f..50aed5ad 100644 --- a/target/nextflow/filter/filter_with_counts/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_counts/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_with_counts" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -280,7 +280,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -321,11 +321,11 @@ build_info: output: "target/nextflow/filter/filter_with_counts" executable: "target/nextflow/filter/filter_with_counts/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -355,7 +355,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/filter_with_counts/main.nf b/target/nextflow/filter/filter_with_counts/main.nf index b4d1a98a..46b28125 100644 --- a/target/nextflow/filter/filter_with_counts/main.nf +++ b/target/nextflow/filter/filter_with_counts/main.nf @@ -1,4 +1,4 @@ -// filter_with_counts v4.0.1 +// filter_with_counts v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "filter_with_counts", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3392,7 +3392,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3448,12 +3448,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/filter_with_counts", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3478,7 +3478,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4050,7 +4050,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/filter_with_counts", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/filter/filter_with_counts/nextflow.config b/target/nextflow/filter/filter_with_counts/nextflow.config index 648e1c81..18457208 100644 --- a/target/nextflow/filter/filter_with_counts/nextflow.config +++ b/target/nextflow/filter/filter_with_counts/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/filter_with_counts' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Filter scRNA-seq data based on the primary QC metrics. \nThis is based on both the UMI counts, the gene counts \nand the mitochondrial genes (genes starting with mt/MT).\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml b/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml index 12c15ce3..b0b7fa6b 100644 --- a/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_pattern/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_with_pattern" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -211,7 +211,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -246,11 +246,11 @@ build_info: output: "target/nextflow/filter/filter_with_pattern" executable: "target/nextflow/filter/filter_with_pattern/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/filter_with_pattern/main.nf b/target/nextflow/filter/filter_with_pattern/main.nf index 5942e113..c6c2de92 100644 --- a/target/nextflow/filter/filter_with_pattern/main.nf +++ b/target/nextflow/filter/filter_with_pattern/main.nf @@ -1,4 +1,4 @@ -// filter_with_pattern v4.0.1 +// filter_with_pattern v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "filter_with_pattern", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3302,7 +3302,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3348,12 +3348,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/filter_with_pattern", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3378,7 +3378,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3877,7 +3877,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/filter_with_pattern", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/filter/filter_with_pattern/nextflow.config b/target/nextflow/filter/filter_with_pattern/nextflow.config index 70692eaa..f39ad713 100644 --- a/target/nextflow/filter/filter_with_pattern/nextflow.config +++ b/target/nextflow/filter/filter_with_pattern/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/filter_with_pattern' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Filter a MuData object based on gene names using a regex.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml index 72e1a60d..3b33f09e 100644 --- a/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/nextflow/filter/filter_with_scrublet/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_with_scrublet" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -333,7 +333,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -378,11 +378,11 @@ build_info: output: "target/nextflow/filter/filter_with_scrublet" executable: "target/nextflow/filter/filter_with_scrublet/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -412,7 +412,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/filter_with_scrublet/main.nf b/target/nextflow/filter/filter_with_scrublet/main.nf index ad550566..cf79f99d 100644 --- a/target/nextflow/filter/filter_with_scrublet/main.nf +++ b/target/nextflow/filter/filter_with_scrublet/main.nf @@ -1,4 +1,4 @@ -// filter_with_scrublet v4.0.1 +// filter_with_scrublet v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "filter_with_scrublet", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3429,7 +3429,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3489,12 +3489,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/filter_with_scrublet", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3519,7 +3519,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4065,7 +4065,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/filter_with_scrublet", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highcpu", diff --git a/target/nextflow/filter/filter_with_scrublet/nextflow.config b/target/nextflow/filter/filter_with_scrublet/nextflow.config index dab10088..533aa1c5 100644 --- a/target/nextflow/filter/filter_with_scrublet/nextflow.config +++ b/target/nextflow/filter/filter_with_scrublet/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/filter_with_scrublet' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Doublet detection using the Scrublet method (Wolock, Lopez and Klein, 2019).\nThe method tests for potential doublets by using the expression profiles of\ncells to generate synthetic potential doubles which are tested against cells. \nThe method returns a "doublet score" on which it calls for potential doublets.\n\nFor the source code please visit https://github.com/AllonKleinLab/scrublet.\n\nFor 10x we expect the doublet rates to be:\n Multiplet Rate (%) - # of Cells Loaded - # of Cells Recovered\n ~0.4% ~800 ~500\n ~0.8% ~1,600 ~1,000\n ~1.6% ~3,200 ~2,000\n ~2.3% ~4,800 ~3,000\n ~3.1% ~6,400 ~4,000\n ~3.9% ~8,000 ~5,000\n ~4.6% ~9,600 ~6,000\n ~5.4% ~11,200 ~7,000\n ~6.1% ~12,800 ~8,000\n ~6.9% ~14,400 ~9,000\n ~7.6% ~16,000 ~10,000\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/filter/intersect_obs/.config.vsh.yaml b/target/nextflow/filter/intersect_obs/.config.vsh.yaml index 1272f152..36cbe402 100644 --- a/target/nextflow/filter/intersect_obs/.config.vsh.yaml +++ b/target/nextflow/filter/intersect_obs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "intersect_obs" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -183,7 +183,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -218,11 +218,11 @@ build_info: output: "target/nextflow/filter/intersect_obs" executable: "target/nextflow/filter/intersect_obs/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -252,7 +252,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/intersect_obs/main.nf b/target/nextflow/filter/intersect_obs/main.nf index 716919ce..74f4363b 100644 --- a/target/nextflow/filter/intersect_obs/main.nf +++ b/target/nextflow/filter/intersect_obs/main.nf @@ -1,4 +1,4 @@ -// intersect_obs v4.0.1 +// intersect_obs v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "intersect_obs", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3274,7 +3274,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3320,12 +3320,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/intersect_obs", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3350,7 +3350,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3857,7 +3857,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/intersect_obs", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/filter/intersect_obs/nextflow.config b/target/nextflow/filter/intersect_obs/nextflow.config index 4ed478ad..2fe2ff34 100644 --- a/target/nextflow/filter/intersect_obs/nextflow.config +++ b/target/nextflow/filter/intersect_obs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/intersect_obs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Create an intersection between two or more modalities.\n\nThis component removes any observations which are not present in all modalities.\n' author = 'Dries Schaumont, Isabelle Bergiers' } diff --git a/target/nextflow/filter/remove_modality/.config.vsh.yaml b/target/nextflow/filter/remove_modality/.config.vsh.yaml index 0192d113..1bbf6b70 100644 --- a/target/nextflow/filter/remove_modality/.config.vsh.yaml +++ b/target/nextflow/filter/remove_modality/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "remove_modality" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -163,7 +163,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,11 @@ build_info: output: "target/nextflow/filter/remove_modality" executable: "target/nextflow/filter/remove_modality/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -232,7 +232,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/remove_modality/main.nf b/target/nextflow/filter/remove_modality/main.nf index 2675bef8..ad948a88 100644 --- a/target/nextflow/filter/remove_modality/main.nf +++ b/target/nextflow/filter/remove_modality/main.nf @@ -1,4 +1,4 @@ -// remove_modality v4.0.1 +// remove_modality v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "remove_modality", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3241,7 +3241,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3287,12 +3287,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/remove_modality", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3317,7 +3317,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3774,7 +3774,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/remove_modality", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/filter/remove_modality/nextflow.config b/target/nextflow/filter/remove_modality/nextflow.config index 29cdea4f..d1411e5c 100644 --- a/target/nextflow/filter/remove_modality/nextflow.config +++ b/target/nextflow/filter/remove_modality/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/remove_modality' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Remove a modality from a .h5mu file\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml index 374cb0cd..3d49d23f 100644 --- a/target/nextflow/filter/subset_h5mu/.config.vsh.yaml +++ b/target/nextflow/filter/subset_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "subset_h5mu" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -177,7 +177,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -212,11 +212,11 @@ build_info: output: "target/nextflow/filter/subset_h5mu" executable: "target/nextflow/filter/subset_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -246,7 +246,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/subset_h5mu/main.nf b/target/nextflow/filter/subset_h5mu/main.nf index 411bc4a7..d4c97784 100644 --- a/target/nextflow/filter/subset_h5mu/main.nf +++ b/target/nextflow/filter/subset_h5mu/main.nf @@ -1,4 +1,4 @@ -// subset_h5mu v4.0.1 +// subset_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "subset_h5mu", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3260,7 +3260,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3306,12 +3306,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/subset_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3336,7 +3336,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3797,7 +3797,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/subset_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/filter/subset_h5mu/nextflow.config b/target/nextflow/filter/subset_h5mu/nextflow.config index 665eb90a..5c980b27 100644 --- a/target/nextflow/filter/subset_h5mu/nextflow.config +++ b/target/nextflow/filter/subset_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/subset_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Create a subset of a mudata file by selecting the first number of observations\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/filter/subset_obsp/.config.vsh.yaml b/target/nextflow/filter/subset_obsp/.config.vsh.yaml index 6bbded93..3da3482a 100644 --- a/target/nextflow/filter/subset_obsp/.config.vsh.yaml +++ b/target/nextflow/filter/subset_obsp/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "subset_obsp" namespace: "filter" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -207,7 +207,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -248,11 +248,11 @@ build_info: output: "target/nextflow/filter/subset_obsp" executable: "target/nextflow/filter/subset_obsp/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -282,7 +282,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/filter/subset_obsp/main.nf b/target/nextflow/filter/subset_obsp/main.nf index 7d71c4a3..7bd29e0e 100644 --- a/target/nextflow/filter/subset_obsp/main.nf +++ b/target/nextflow/filter/subset_obsp/main.nf @@ -1,4 +1,4 @@ -// subset_obsp v4.0.1 +// subset_obsp v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "subset_obsp", "namespace" : "filter", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3298,7 +3298,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3354,12 +3354,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/filter/subset_obsp", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3384,7 +3384,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3872,7 +3872,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/filter/subset_obsp", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/filter/subset_obsp/nextflow.config b/target/nextflow/filter/subset_obsp/nextflow.config index e2bba2cd..bc26ddfa 100644 --- a/target/nextflow/filter/subset_obsp/nextflow.config +++ b/target/nextflow/filter/subset_obsp/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'filter/subset_obsp' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Create a subset of an .obsp field in a mudata file, by filtering the columns based on the values of an .obs column. The resulting subset is moved to an .obsm slot.\n' author = 'Dorien Roosen' } diff --git a/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml b/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml index d4f1befb..687fd801 100644 --- a/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/bcftools/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bcftools" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -195,11 +195,11 @@ build_info: output: "target/nextflow/genetic_demux/bcftools" executable: "target/nextflow/genetic_demux/bcftools/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -229,7 +229,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/bcftools/main.nf b/target/nextflow/genetic_demux/bcftools/main.nf index caa6d63f..b5c7b309 100644 --- a/target/nextflow/genetic_demux/bcftools/main.nf +++ b/target/nextflow/genetic_demux/bcftools/main.nf @@ -1,4 +1,4 @@ -// bcftools v4.0.1 +// bcftools v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bcftools", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3236,7 +3236,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3278,12 +3278,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/bcftools", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3308,7 +3308,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3765,7 +3765,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/bcftools", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/genetic_demux/bcftools/nextflow.config b/target/nextflow/genetic_demux/bcftools/nextflow.config index d85ef813..d9ae5750 100644 --- a/target/nextflow/genetic_demux/bcftools/nextflow.config +++ b/target/nextflow/genetic_demux/bcftools/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/bcftools' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Filter the variants called by freebayes or cellSNP' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml b/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml index c7be5974..e3026855 100644 --- a/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/cellsnp/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellsnp" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -327,7 +327,7 @@ engines: id: "docker" image: "ubuntu:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -369,11 +369,11 @@ build_info: output: "target/nextflow/genetic_demux/cellsnp" executable: "target/nextflow/genetic_demux/cellsnp/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -403,7 +403,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/cellsnp/main.nf b/target/nextflow/genetic_demux/cellsnp/main.nf index 38f1edc0..37584276 100644 --- a/target/nextflow/genetic_demux/cellsnp/main.nf +++ b/target/nextflow/genetic_demux/cellsnp/main.nf @@ -1,4 +1,4 @@ -// cellsnp v4.0.1 +// cellsnp v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellsnp", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3424,7 +3424,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3473,12 +3473,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/cellsnp", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3503,7 +3503,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3993,7 +3993,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/cellsnp", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/genetic_demux/cellsnp/nextflow.config b/target/nextflow/genetic_demux/cellsnp/nextflow.config index 097ce677..5b7c489a 100644 --- a/target/nextflow/genetic_demux/cellsnp/nextflow.config +++ b/target/nextflow/genetic_demux/cellsnp/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/cellsnp' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'cellSNP aims to pileup the expressed alleles in single-cell or bulk RNA-seq data. It can be directly used for donor deconvolution in multiplexed single-cell RNA-seq data, particularly with vireo.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml b/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml index 9b8738bf..d5029a32 100644 --- a/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/demuxlet/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "demuxlet" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -455,11 +455,11 @@ build_info: output: "target/nextflow/genetic_demux/demuxlet" executable: "target/nextflow/genetic_demux/demuxlet/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -489,7 +489,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/demuxlet/main.nf b/target/nextflow/genetic_demux/demuxlet/main.nf index c208d2db..a54757c6 100644 --- a/target/nextflow/genetic_demux/demuxlet/main.nf +++ b/target/nextflow/genetic_demux/demuxlet/main.nf @@ -1,4 +1,4 @@ -// demuxlet v4.0.1 +// demuxlet v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "demuxlet", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3523,7 +3523,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3584,12 +3584,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/demuxlet", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3614,7 +3614,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4174,7 +4174,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/demuxlet", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/genetic_demux/demuxlet/nextflow.config b/target/nextflow/genetic_demux/demuxlet/nextflow.config index 3c8784a0..39e5a455 100644 --- a/target/nextflow/genetic_demux/demuxlet/nextflow.config +++ b/target/nextflow/genetic_demux/demuxlet/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/demuxlet' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Demuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping data\nfor each sample is available (e.g. from SNP arrays), demuxlet would be recommended. Be careful\nthat the parameters on the github is not in line with the newest help version.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml b/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml index a9bed8e3..46d190dd 100644 --- a/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/dsc_pileup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "dsc_pileup" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -329,7 +329,7 @@ engines: id: "docker" image: "ubuntu:20.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -367,11 +367,11 @@ build_info: output: "target/nextflow/genetic_demux/dsc_pileup" executable: "target/nextflow/genetic_demux/dsc_pileup/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -401,7 +401,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/dsc_pileup/main.nf b/target/nextflow/genetic_demux/dsc_pileup/main.nf index 45cd4cef..234d114c 100644 --- a/target/nextflow/genetic_demux/dsc_pileup/main.nf +++ b/target/nextflow/genetic_demux/dsc_pileup/main.nf @@ -1,4 +1,4 @@ -// dsc_pileup v4.0.1 +// dsc_pileup v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "dsc_pileup", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3432,7 +3432,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:20.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3477,12 +3477,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/dsc_pileup", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3507,7 +3507,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3992,7 +3992,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/dsc_pileup", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/genetic_demux/dsc_pileup/nextflow.config b/target/nextflow/genetic_demux/dsc_pileup/nextflow.config index f9a5e8c0..de9eb114 100644 --- a/target/nextflow/genetic_demux/dsc_pileup/nextflow.config +++ b/target/nextflow/genetic_demux/dsc_pileup/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/dsc_pileup' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Dsc-pileup is a software tool to pileup reads and corresponding base quality \nfor each overlapping SNPs and each barcode. By using pileup files,\nit would allow us to run demuxlet/freemuxlet pretty fast multiple times\nwithout going over the BAM file again.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml b/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml index b3713264..304de5cf 100644 --- a/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/freebayes/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "freebayes" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -774,7 +774,7 @@ engines: id: "docker" image: "debian:latest" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -792,11 +792,11 @@ build_info: output: "target/nextflow/genetic_demux/freebayes" executable: "target/nextflow/genetic_demux/freebayes/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -826,7 +826,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/freebayes/main.nf b/target/nextflow/genetic_demux/freebayes/main.nf index 9a4d4639..3a3db50e 100644 --- a/target/nextflow/genetic_demux/freebayes/main.nf +++ b/target/nextflow/genetic_demux/freebayes/main.nf @@ -1,4 +1,4 @@ -// freebayes v4.0.1 +// freebayes v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "freebayes", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3891,7 +3891,7 @@ meta = [ "id" : "docker", "image" : "debian:latest", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3914,12 +3914,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/freebayes", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3944,7 +3944,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4542,7 +4542,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/freebayes", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/genetic_demux/freebayes/nextflow.config b/target/nextflow/genetic_demux/freebayes/nextflow.config index 0ca73915..016dd6da 100644 --- a/target/nextflow/genetic_demux/freebayes/nextflow.config +++ b/target/nextflow/genetic_demux/freebayes/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/freebayes' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Freebayes is a Bayesian genetic variant detector designed to\nfind small polymorphisms, specifically SNPs.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml b/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml index dcd20749..43bf4988 100644 --- a/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/freemuxlet/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "freemuxlet" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -322,7 +322,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -371,11 +371,11 @@ build_info: output: "target/nextflow/genetic_demux/freemuxlet" executable: "target/nextflow/genetic_demux/freemuxlet/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -405,7 +405,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/freemuxlet/main.nf b/target/nextflow/genetic_demux/freemuxlet/main.nf index 37a742a5..ef394de0 100644 --- a/target/nextflow/genetic_demux/freemuxlet/main.nf +++ b/target/nextflow/genetic_demux/freemuxlet/main.nf @@ -1,4 +1,4 @@ -// freemuxlet v4.0.1 +// freemuxlet v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "freemuxlet", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3428,7 +3428,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3489,12 +3489,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/freemuxlet", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3519,7 +3519,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4072,7 +4072,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/freemuxlet", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/genetic_demux/freemuxlet/nextflow.config b/target/nextflow/genetic_demux/freemuxlet/nextflow.config index 33779a4b..51fd5748 100644 --- a/target/nextflow/genetic_demux/freemuxlet/nextflow.config +++ b/target/nextflow/genetic_demux/freemuxlet/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/freemuxlet' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Freemuxlet is a software tool to deconvolute sample identity and identify multiplets when\nmultiple samples are pooled by barcoded single cell sequencing. If external genotyping\ndata is not available, the genotyping-free version demuxlet, freemuxlet, would be recommended.\n' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/samtools/.config.vsh.yaml b/target/nextflow/genetic_demux/samtools/.config.vsh.yaml index 4a33ad83..be0b912d 100644 --- a/target/nextflow/genetic_demux/samtools/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/samtools/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -138,7 +138,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -173,11 +173,11 @@ build_info: output: "target/nextflow/genetic_demux/samtools" executable: "target/nextflow/genetic_demux/samtools/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -207,7 +207,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/samtools/main.nf b/target/nextflow/genetic_demux/samtools/main.nf index 85cbf737..51690a33 100644 --- a/target/nextflow/genetic_demux/samtools/main.nf +++ b/target/nextflow/genetic_demux/samtools/main.nf @@ -1,4 +1,4 @@ -// samtools v4.0.1 +// samtools v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3212,7 +3212,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3256,12 +3256,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/samtools", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3286,7 +3286,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3730,7 +3730,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/samtools", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/genetic_demux/samtools/nextflow.config b/target/nextflow/genetic_demux/samtools/nextflow.config index a6e77f84..dd13f3e7 100644 --- a/target/nextflow/genetic_demux/samtools/nextflow.config +++ b/target/nextflow/genetic_demux/samtools/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/samtools' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Filter the BAM according to the instruction of scSplit via Samtools.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml b/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml index e65dcd3e..46cc49f6 100644 --- a/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/scsplit/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scsplit" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -265,7 +265,7 @@ engines: id: "docker" image: "python:3.13" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -301,11 +301,11 @@ build_info: output: "target/nextflow/genetic_demux/scsplit" executable: "target/nextflow/genetic_demux/scsplit/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -335,7 +335,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/scsplit/main.nf b/target/nextflow/genetic_demux/scsplit/main.nf index 33de5a09..4fc184a8 100644 --- a/target/nextflow/genetic_demux/scsplit/main.nf +++ b/target/nextflow/genetic_demux/scsplit/main.nf @@ -1,4 +1,4 @@ -// scsplit v4.0.1 +// scsplit v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scsplit", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3355,7 +3355,7 @@ meta = [ "id" : "docker", "image" : "python:3.13", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3404,12 +3404,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/scsplit", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3434,7 +3434,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3921,7 +3921,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/scsplit", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/genetic_demux/scsplit/nextflow.config b/target/nextflow/genetic_demux/scsplit/nextflow.config index d7467f4f..a942e28f 100644 --- a/target/nextflow/genetic_demux/scsplit/nextflow.config +++ b/target/nextflow/genetic_demux/scsplit/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/scsplit' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'scsplit is a genotype-free demultiplexing methode of pooled single-cell RNA-seq, using a hidden state model for identifying genetically distinct samples within a mixed population.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml b/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml index 02231b4b..b1a7cd8d 100644 --- a/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/souporcell/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "souporcell" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -272,7 +272,7 @@ engines: id: "docker" image: "cumulusprod/souporcell:2022.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" entrypoint: [] cmd: null @@ -285,11 +285,11 @@ build_info: output: "target/nextflow/genetic_demux/souporcell" executable: "target/nextflow/genetic_demux/souporcell/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -319,7 +319,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/souporcell/main.nf b/target/nextflow/genetic_demux/souporcell/main.nf index fa9af5bb..2b1ce816 100644 --- a/target/nextflow/genetic_demux/souporcell/main.nf +++ b/target/nextflow/genetic_demux/souporcell/main.nf @@ -1,4 +1,4 @@ -// souporcell v4.0.1 +// souporcell v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "souporcell", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3362,7 +3362,7 @@ meta = [ "id" : "docker", "image" : "cumulusprod/souporcell:2022.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/" }, { @@ -3376,12 +3376,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/souporcell", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3406,7 +3406,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3888,7 +3888,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/souporcell", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/genetic_demux/souporcell/nextflow.config b/target/nextflow/genetic_demux/souporcell/nextflow.config index c4c09d58..e87bbeac 100644 --- a/target/nextflow/genetic_demux/souporcell/nextflow.config +++ b/target/nextflow/genetic_demux/souporcell/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/souporcell' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'souporcell is a method for clustering mixed-genotype scRNAseq experiments by individual.' author = 'Xichen Wu' } diff --git a/target/nextflow/genetic_demux/vireo/.config.vsh.yaml b/target/nextflow/genetic_demux/vireo/.config.vsh.yaml index b90670e8..3e01cff6 100644 --- a/target/nextflow/genetic_demux/vireo/.config.vsh.yaml +++ b/target/nextflow/genetic_demux/vireo/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "vireo" namespace: "genetic_demux" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Xichen Wu" roles: @@ -285,7 +285,7 @@ engines: id: "docker" image: "python:3.13" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -305,11 +305,11 @@ build_info: output: "target/nextflow/genetic_demux/vireo" executable: "target/nextflow/genetic_demux/vireo/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -339,7 +339,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/genetic_demux/vireo/main.nf b/target/nextflow/genetic_demux/vireo/main.nf index 5f81a577..16120830 100644 --- a/target/nextflow/genetic_demux/vireo/main.nf +++ b/target/nextflow/genetic_demux/vireo/main.nf @@ -1,4 +1,4 @@ -// vireo v4.0.1 +// vireo v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "vireo", "namespace" : "genetic_demux", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Xichen Wu", @@ -3382,7 +3382,7 @@ meta = [ "id" : "docker", "image" : "python:3.13", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3407,12 +3407,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/genetic_demux/vireo", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3437,7 +3437,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3921,7 +3921,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/genetic_demux/vireo", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/genetic_demux/vireo/nextflow.config b/target/nextflow/genetic_demux/vireo/nextflow.config index 8ae33c7f..681f6995 100644 --- a/target/nextflow/genetic_demux/vireo/nextflow.config +++ b/target/nextflow/genetic_demux/vireo/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'genetic_demux/vireo' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Vireo is primarily designed for demultiplexing cells into donors by modelling of expressed alleles.' author = 'Xichen Wu' } diff --git a/target/nextflow/integrate/harmonypy/.config.vsh.yaml b/target/nextflow/integrate/harmonypy/.config.vsh.yaml index c477b328..1c9e5814 100644 --- a/target/nextflow/integrate/harmonypy/.config.vsh.yaml +++ b/target/nextflow/integrate/harmonypy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "harmonypy" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -232,7 +232,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -275,11 +275,11 @@ build_info: output: "target/nextflow/integrate/harmonypy" executable: "target/nextflow/integrate/harmonypy/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -309,7 +309,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/integrate/harmonypy/main.nf b/target/nextflow/integrate/harmonypy/main.nf index ec839cac..7b35cb6b 100644 --- a/target/nextflow/integrate/harmonypy/main.nf +++ b/target/nextflow/integrate/harmonypy/main.nf @@ -1,4 +1,4 @@ -// harmonypy v4.0.1 +// harmonypy v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "harmonypy", "namespace" : "integrate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3330,7 +3330,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3388,12 +3388,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/integrate/harmonypy", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3418,7 +3418,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3904,7 +3904,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/integrate/harmonypy", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/integrate/harmonypy/nextflow.config b/target/nextflow/integrate/harmonypy/nextflow.config index 812df357..8f8465ab 100644 --- a/target/nextflow/integrate/harmonypy/nextflow.config +++ b/target/nextflow/integrate/harmonypy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/harmonypy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs Harmony integration based as described in https://github.com/immunogenomics/harmony. Based on an implementation in python from https://github.com/slowkow/harmonypy' author = 'Dries Schaumont, Robrecht Cannoodt' } diff --git a/target/nextflow/integrate/scanorama/.config.vsh.yaml b/target/nextflow/integrate/scanorama/.config.vsh.yaml index 03d37e1d..9e068b2a 100644 --- a/target/nextflow/integrate/scanorama/.config.vsh.yaml +++ b/target/nextflow/integrate/scanorama/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanorama" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -269,7 +269,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -313,11 +313,11 @@ build_info: output: "target/nextflow/integrate/scanorama" executable: "target/nextflow/integrate/scanorama/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -347,7 +347,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/integrate/scanorama/main.nf b/target/nextflow/integrate/scanorama/main.nf index 14978e3e..3ee3ff78 100644 --- a/target/nextflow/integrate/scanorama/main.nf +++ b/target/nextflow/integrate/scanorama/main.nf @@ -1,4 +1,4 @@ -// scanorama v4.0.1 +// scanorama v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scanorama", "namespace" : "integrate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3374,7 +3374,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3433,12 +3433,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/integrate/scanorama", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3463,7 +3463,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3957,7 +3957,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/integrate/scanorama", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midcpu", diff --git a/target/nextflow/integrate/scanorama/nextflow.config b/target/nextflow/integrate/scanorama/nextflow.config index f4969b02..5cef26e5 100644 --- a/target/nextflow/integrate/scanorama/nextflow.config +++ b/target/nextflow/integrate/scanorama/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/scanorama' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Use Scanorama to integrate different experiments.\n' author = 'Dries De Maeyer, Dries Schaumont' } diff --git a/target/nextflow/integrate/scarches/.config.vsh.yaml b/target/nextflow/integrate/scarches/.config.vsh.yaml index 3b748dab..f8ac630b 100644 --- a/target/nextflow/integrate/scarches/.config.vsh.yaml +++ b/target/nextflow/integrate/scarches/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scarches" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -442,7 +442,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -474,11 +474,11 @@ build_info: output: "target/nextflow/integrate/scarches" executable: "target/nextflow/integrate/scarches/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -508,7 +508,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/integrate/scarches/main.nf b/target/nextflow/integrate/scarches/main.nf index 06b37666..1bee232d 100644 --- a/target/nextflow/integrate/scarches/main.nf +++ b/target/nextflow/integrate/scarches/main.nf @@ -1,4 +1,4 @@ -// scarches v4.0.1 +// scarches v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scarches", "namespace" : "integrate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3567,7 +3567,7 @@ meta = [ "id" : "docker", "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3607,12 +3607,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/integrate/scarches", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3637,7 +3637,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4465,7 +4465,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/integrate/scarches", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/integrate/scarches/nextflow.config b/target/nextflow/integrate/scarches/nextflow.config index 6e5a9b29..96b21af6 100644 --- a/target/nextflow/integrate/scarches/nextflow.config +++ b/target/nextflow/integrate/scarches/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/scarches' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs reference mapping with scArches' author = 'Vladimir Shitov, Dorien Roosen' } diff --git a/target/nextflow/integrate/scvi/.config.vsh.yaml b/target/nextflow/integrate/scvi/.config.vsh.yaml index fbd0e07e..fc8affca 100644 --- a/target/nextflow/integrate/scvi/.config.vsh.yaml +++ b/target/nextflow/integrate/scvi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvi" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Malte D. Luecken" roles: @@ -563,7 +563,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -600,11 +600,11 @@ build_info: output: "target/nextflow/integrate/scvi" executable: "target/nextflow/integrate/scvi/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -634,7 +634,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/integrate/scvi/main.nf b/target/nextflow/integrate/scvi/main.nf index 50615866..69198843 100644 --- a/target/nextflow/integrate/scvi/main.nf +++ b/target/nextflow/integrate/scvi/main.nf @@ -1,4 +1,4 @@ -// scvi v4.0.1 +// scvi v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scvi", "namespace" : "integrate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Malte D. Luecken", @@ -3714,7 +3714,7 @@ meta = [ "id" : "docker", "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3762,12 +3762,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/integrate/scvi", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3792,7 +3792,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4388,7 +4388,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/integrate/scvi", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midcpu", diff --git a/target/nextflow/integrate/scvi/nextflow.config b/target/nextflow/integrate/scvi/nextflow.config index 97fc8ea8..b9d94eaa 100644 --- a/target/nextflow/integrate/scvi/nextflow.config +++ b/target/nextflow/integrate/scvi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/scvi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs scvi integration as done in the human lung cell atlas https://github.com/LungCellAtlas/HLCA' author = 'Malte D. Luecken, Dries Schaumont, Matthias Beyens' } diff --git a/target/nextflow/integrate/totalvi/.config.vsh.yaml b/target/nextflow/integrate/totalvi/.config.vsh.yaml index 06c91439..493592fa 100644 --- a/target/nextflow/integrate/totalvi/.config.vsh.yaml +++ b/target/nextflow/integrate/totalvi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -484,7 +484,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -517,11 +517,11 @@ build_info: output: "target/nextflow/integrate/totalvi" executable: "target/nextflow/integrate/totalvi/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -551,7 +551,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/integrate/totalvi/main.nf b/target/nextflow/integrate/totalvi/main.nf index 07a9c971..1cc1815c 100644 --- a/target/nextflow/integrate/totalvi/main.nf +++ b/target/nextflow/integrate/totalvi/main.nf @@ -1,4 +1,4 @@ -// totalvi v4.0.1 +// totalvi v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "totalvi", "namespace" : "integrate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3601,7 +3601,7 @@ meta = [ "id" : "docker", "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3642,12 +3642,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/integrate/totalvi", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3672,7 +3672,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4314,7 +4314,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/integrate/totalvi", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/integrate/totalvi/nextflow.config b/target/nextflow/integrate/totalvi/nextflow.config index 089dde41..9c4650d8 100644 --- a/target/nextflow/integrate/totalvi/nextflow.config +++ b/target/nextflow/integrate/totalvi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/totalvi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs TotalVI integration of CITE-seq and scRNA-seq data.' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml b/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml index 636afe7a..8ab648fe 100644 --- a/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml +++ b/target/nextflow/integrate/totalvi_scarches/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi_scarches" namespace: "integrate" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" info: @@ -353,7 +353,7 @@ engines: id: "docker" image: "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -385,11 +385,11 @@ build_info: output: "target/nextflow/integrate/totalvi_scarches" executable: "target/nextflow/integrate/totalvi_scarches/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -419,7 +419,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/integrate/totalvi_scarches/main.nf b/target/nextflow/integrate/totalvi_scarches/main.nf index 0e8afd2f..5f03d1f8 100644 --- a/target/nextflow/integrate/totalvi_scarches/main.nf +++ b/target/nextflow/integrate/totalvi_scarches/main.nf @@ -1,4 +1,4 @@ -// totalvi_scarches v4.0.1 +// totalvi_scarches v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "totalvi_scarches", "namespace" : "integrate", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3457,7 +3457,7 @@ meta = [ "id" : "docker", "image" : "pytorch/pytorch:2.9.1-cuda12.8-cudnn9-runtime", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3497,12 +3497,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/integrate/totalvi_scarches", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3527,7 +3527,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4179,7 +4179,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/integrate/totalvi_scarches", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/integrate/totalvi_scarches/nextflow.config b/target/nextflow/integrate/totalvi_scarches/nextflow.config index 33eccfc4..e05fcafe 100644 --- a/target/nextflow/integrate/totalvi_scarches/nextflow.config +++ b/target/nextflow/integrate/totalvi_scarches/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integrate/totalvi_scarches' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs totalVI integration by mapping the query dataset to a reference dataset or model. \n' author = 'Vladimir Shitov' } diff --git a/target/nextflow/interpret/lianapy/.config.vsh.yaml b/target/nextflow/interpret/lianapy/.config.vsh.yaml index ca46989a..61b2b11c 100644 --- a/target/nextflow/interpret/lianapy/.config.vsh.yaml +++ b/target/nextflow/interpret/lianapy/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "lianapy" namespace: "interpret" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Mauro Saporita" roles: @@ -320,7 +320,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -357,11 +357,11 @@ build_info: output: "target/nextflow/interpret/lianapy" executable: "target/nextflow/interpret/lianapy/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -391,7 +391,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/interpret/lianapy/main.nf b/target/nextflow/interpret/lianapy/main.nf index 75de9a06..96e91b5c 100644 --- a/target/nextflow/interpret/lianapy/main.nf +++ b/target/nextflow/interpret/lianapy/main.nf @@ -1,4 +1,4 @@ -// lianapy v4.0.1 +// lianapy v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "lianapy", "namespace" : "interpret", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Mauro Saporita", @@ -3421,7 +3421,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3469,12 +3469,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/interpret/lianapy", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3499,7 +3499,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4020,7 +4020,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/interpret/lianapy", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/interpret/lianapy/nextflow.config b/target/nextflow/interpret/lianapy/nextflow.config index 6d9c30ee..9297e385 100644 --- a/target/nextflow/interpret/lianapy/nextflow.config +++ b/target/nextflow/interpret/lianapy/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'interpret/lianapy' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs LIANA integration based as described in https://github.com/saezlab/liana-py' author = 'Mauro Saporita, Povilas Gibas' } diff --git a/target/nextflow/labels_transfer/knn/.config.vsh.yaml b/target/nextflow/labels_transfer/knn/.config.vsh.yaml index 715f1a27..3bff5dfd 100644 --- a/target/nextflow/labels_transfer/knn/.config.vsh.yaml +++ b/target/nextflow/labels_transfer/knn/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "knn" namespace: "labels_transfer" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -406,7 +406,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -455,11 +455,11 @@ build_info: output: "target/nextflow/labels_transfer/knn" executable: "target/nextflow/labels_transfer/knn/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -489,7 +489,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/labels_transfer/knn/main.nf b/target/nextflow/labels_transfer/knn/main.nf index 11ab592a..54012cb8 100644 --- a/target/nextflow/labels_transfer/knn/main.nf +++ b/target/nextflow/labels_transfer/knn/main.nf @@ -1,4 +1,4 @@ -// knn v4.0.1 +// knn v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "knn", "namespace" : "labels_transfer", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3534,7 +3534,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3601,12 +3601,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/labels_transfer/knn", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3631,7 +3631,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4235,7 +4235,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/labels_transfer/knn", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/labels_transfer/knn/nextflow.config b/target/nextflow/labels_transfer/knn/nextflow.config index 0b8cd78f..bd839084 100644 --- a/target/nextflow/labels_transfer/knn/nextflow.config +++ b/target/nextflow/labels_transfer/knn/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'labels_transfer/knn' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component performs label transfer from reference to query using a K-Neirest Neighbors classifier.\n' author = 'Dorien Roosen, Vladimir Shitov' } diff --git a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml index 94f380f3..d307d0fd 100644 --- a/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml +++ b/target/nextflow/labels_transfer/xgboost/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "xgboost" namespace: "labels_transfer" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -555,7 +555,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -604,11 +604,11 @@ build_info: output: "target/nextflow/labels_transfer/xgboost" executable: "target/nextflow/labels_transfer/xgboost/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -638,7 +638,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/labels_transfer/xgboost/main.nf b/target/nextflow/labels_transfer/xgboost/main.nf index 0c8ed37e..5caa510f 100644 --- a/target/nextflow/labels_transfer/xgboost/main.nf +++ b/target/nextflow/labels_transfer/xgboost/main.nf @@ -1,4 +1,4 @@ -// xgboost v4.0.1 +// xgboost v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "xgboost", "namespace" : "labels_transfer", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3697,7 +3697,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3763,12 +3763,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/labels_transfer/xgboost", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3793,7 +3793,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4657,7 +4657,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/labels_transfer/xgboost", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/labels_transfer/xgboost/nextflow.config b/target/nextflow/labels_transfer/xgboost/nextflow.config index a3a86ae9..89b19568 100644 --- a/target/nextflow/labels_transfer/xgboost/nextflow.config +++ b/target/nextflow/labels_transfer/xgboost/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'labels_transfer/xgboost' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs label transfer from reference to query using XGBoost classifier' author = 'Vladimir Shitov' } diff --git a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml index 21b948b1..a69c05c9 100644 --- a/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml +++ b/target/nextflow/mapping/bd_rhapsody/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -1098,7 +1098,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -1125,11 +1125,11 @@ build_info: output: "target/nextflow/mapping/bd_rhapsody" executable: "target/nextflow/mapping/bd_rhapsody/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -1159,7 +1159,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/bd_rhapsody/main.nf b/target/nextflow/mapping/bd_rhapsody/main.nf index 7e2728db..cff64950 100644 --- a/target/nextflow/mapping/bd_rhapsody/main.nf +++ b/target/nextflow/mapping/bd_rhapsody/main.nf @@ -1,4 +1,4 @@ -// bd_rhapsody v4.0.1 +// bd_rhapsody v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bd_rhapsody", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -4399,7 +4399,7 @@ meta = [ "id" : "docker", "image" : "bdgenomics/rhapsody:2.2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -4434,12 +4434,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/bd_rhapsody", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -4464,7 +4464,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -5202,7 +5202,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/bd_rhapsody", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/bd_rhapsody/nextflow.config b/target/nextflow/mapping/bd_rhapsody/nextflow.config index 561f152f..bc9d2193 100644 --- a/target/nextflow/mapping/bd_rhapsody/nextflow.config +++ b/target/nextflow/mapping/bd_rhapsody/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/bd_rhapsody' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'BD Rhapsody Sequence Analysis CWL pipeline v2.2.1\n \nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody assay kits, including: Whole Transcriptome\nmRNA, Targeted mRNA, AbSeq Antibody-Oligonucleotides, Single-Cell Multiplexing, TCR/BCR, and\nATAC-Seq\n\nThe CWL pipeline file is obtained by cloning \'https://bitbucket.org/CRSwDev/cwl\' and removing all objects with class \'DockerRequirement\' from the YAML.\n' author = 'Robrecht Cannoodt, Weiwei Schultz' } diff --git a/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml b/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml index 05a85762..c9d55ae2 100644 --- a/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_atac_count/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_atac_count" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -235,7 +235,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger_atac:2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -253,11 +253,11 @@ build_info: output: "target/nextflow/mapping/cellranger_atac_count" executable: "target/nextflow/mapping/cellranger_atac_count/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -287,7 +287,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/cellranger_atac_count/main.nf b/target/nextflow/mapping/cellranger_atac_count/main.nf index 8a60d7cc..d1e88cf4 100644 --- a/target/nextflow/mapping/cellranger_atac_count/main.nf +++ b/target/nextflow/mapping/cellranger_atac_count/main.nf @@ -1,4 +1,4 @@ -// cellranger_atac_count v4.0.1 +// cellranger_atac_count v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_atac_count", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3324,7 +3324,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger_atac:2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3346,12 +3346,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_atac_count", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3376,7 +3376,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3892,7 +3892,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/cellranger_atac_count", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/cellranger_atac_count/nextflow.config b/target/nextflow/mapping/cellranger_atac_count/nextflow.config index 0cfd0f22..4366b437 100644 --- a/target/nextflow/mapping/cellranger_atac_count/nextflow.config +++ b/target/nextflow/mapping/cellranger_atac_count/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_atac_count' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Align fastq files using Cell Ranger ATAC count.' author = 'Vladimir Shitov' } diff --git a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml index fdaf20d6..46bc96fd 100644 --- a/target/nextflow/mapping/cellranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_count/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_count" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -367,7 +367,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -397,11 +397,11 @@ build_info: output: "target/nextflow/mapping/cellranger_count" executable: "target/nextflow/mapping/cellranger_count/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -431,7 +431,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/cellranger_count/main.nf b/target/nextflow/mapping/cellranger_count/main.nf index 89a3b270..e2c6788f 100644 --- a/target/nextflow/mapping/cellranger_count/main.nf +++ b/target/nextflow/mapping/cellranger_count/main.nf @@ -1,4 +1,4 @@ -// cellranger_count v4.0.1 +// cellranger_count v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_count", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3479,7 +3479,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger:9.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3521,12 +3521,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_count", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3551,7 +3551,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4079,7 +4079,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/cellranger_count", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/cellranger_count/nextflow.config b/target/nextflow/mapping/cellranger_count/nextflow.config index 36fe6e29..7379d40b 100644 --- a/target/nextflow/mapping/cellranger_count/nextflow.config +++ b/target/nextflow/mapping/cellranger_count/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_count' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Align fastq files using Cell Ranger count.' author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml index bf3d3f89..fff99326 100644 --- a/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_count_split/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_count_split" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "ubuntu:jammy" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -241,11 +241,11 @@ build_info: output: "target/nextflow/mapping/cellranger_count_split" executable: "target/nextflow/mapping/cellranger_count_split/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -275,7 +275,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/cellranger_count_split/main.nf b/target/nextflow/mapping/cellranger_count_split/main.nf index 76c32866..27ac94a4 100644 --- a/target/nextflow/mapping/cellranger_count_split/main.nf +++ b/target/nextflow/mapping/cellranger_count_split/main.nf @@ -1,4 +1,4 @@ -// cellranger_count_split v4.0.1 +// cellranger_count_split v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_count_split", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3325,7 +3325,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:jammy", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3347,12 +3347,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_count_split", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3377,7 +3377,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3856,7 +3856,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/cellranger_count_split", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/mapping/cellranger_count_split/nextflow.config b/target/nextflow/mapping/cellranger_count_split/nextflow.config index 6d72a8b7..3e0fe5a1 100644 --- a/target/nextflow/mapping/cellranger_count_split/nextflow.config +++ b/target/nextflow/mapping/cellranger_count_split/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_count_split' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Split 10x Cell Ranger output directory into separate output fields.' author = 'Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml index 6ddd5347..41d31a27 100644 --- a/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml +++ b/target/nextflow/mapping/cellranger_multi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_multi" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -952,7 +952,7 @@ engines: id: "docker" image: "quay.io/nf-core/cellranger:10.0.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -991,11 +991,11 @@ build_info: output: "target/nextflow/mapping/cellranger_multi" executable: "target/nextflow/mapping/cellranger_multi/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -1025,7 +1025,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/cellranger_multi/main.nf b/target/nextflow/mapping/cellranger_multi/main.nf index 5fe98978..cf98239e 100644 --- a/target/nextflow/mapping/cellranger_multi/main.nf +++ b/target/nextflow/mapping/cellranger_multi/main.nf @@ -1,4 +1,4 @@ -// cellranger_multi v4.0.1 +// cellranger_multi v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3040,7 +3040,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_multi", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -4080,7 +4080,7 @@ meta = [ "id" : "docker", "image" : "quay.io/nf-core/cellranger:10.0.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -4138,12 +4138,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/cellranger_multi", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -4168,7 +4168,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -5146,7 +5146,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/cellranger_multi", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "veryhighmem", diff --git a/target/nextflow/mapping/cellranger_multi/nextflow.config b/target/nextflow/mapping/cellranger_multi/nextflow.config index 1c607fbe..964b04d1 100644 --- a/target/nextflow/mapping/cellranger_multi/nextflow.config +++ b/target/nextflow/mapping/cellranger_multi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/cellranger_multi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Align fastq files using Cell Ranger multi.' author = 'Dries Schaumont, Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer, Weiwei Schultz, Dorien Roosen' } diff --git a/target/nextflow/mapping/htseq_count/.config.vsh.yaml b/target/nextflow/mapping/htseq_count/.config.vsh.yaml index d8284d4a..39e86b7b 100644 --- a/target/nextflow/mapping/htseq_count/.config.vsh.yaml +++ b/target/nextflow/mapping/htseq_count/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htseq_count" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -396,7 +396,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -422,11 +422,11 @@ build_info: output: "target/nextflow/mapping/htseq_count" executable: "target/nextflow/mapping/htseq_count/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -456,7 +456,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/htseq_count/main.nf b/target/nextflow/mapping/htseq_count/main.nf index 2cf9103a..e938a918 100644 --- a/target/nextflow/mapping/htseq_count/main.nf +++ b/target/nextflow/mapping/htseq_count/main.nf @@ -1,4 +1,4 @@ -// htseq_count v4.0.1 +// htseq_count v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "htseq_count", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3542,7 +3542,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3576,12 +3576,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/htseq_count", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3606,7 +3606,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4181,7 +4181,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/htseq_count", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/htseq_count/nextflow.config b/target/nextflow/mapping/htseq_count/nextflow.config index 8a6b4a8d..31c1fe84 100644 --- a/target/nextflow/mapping/htseq_count/nextflow.config +++ b/target/nextflow/mapping/htseq_count/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/htseq_count' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Quantify gene expression for subsequent testing for differential expression.\n\nThis script takes one or more alignment files in SAM/BAM format and a feature file in GFF format and calculates for each feature the number of reads mapping to it. \n\nSee http://htseq.readthedocs.io/en/master/count.html for details.\n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml index a47481db..03afa657 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/mapping/htseq_count_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htseq_count_to_h5mu" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -201,7 +201,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -236,11 +236,11 @@ build_info: output: "target/nextflow/mapping/htseq_count_to_h5mu" executable: "target/nextflow/mapping/htseq_count_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -270,7 +270,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf index fcaae321..d745fa0e 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/main.nf +++ b/target/nextflow/mapping/htseq_count_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// htseq_count_to_h5mu v4.0.1 +// htseq_count_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "htseq_count_to_h5mu", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3299,7 +3299,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3344,12 +3344,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/htseq_count_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3374,7 +3374,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3936,7 +3936,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/htseq_count_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config b/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config index 84bc5d4c..524880aa 100644 --- a/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config +++ b/target/nextflow/mapping/htseq_count_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/htseq_count_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert the htseq table to a h5mu.\n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/multi_star/.config.vsh.yaml b/target/nextflow/mapping/multi_star/.config.vsh.yaml index d5c49ddc..01d5a3ed 100644 --- a/target/nextflow/mapping/multi_star/.config.vsh.yaml +++ b/target/nextflow/mapping/multi_star/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "multi_star" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2856,7 +2856,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -2904,11 +2904,11 @@ build_info: output: "target/nextflow/mapping/multi_star" executable: "target/nextflow/mapping/multi_star/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -2938,7 +2938,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/multi_star/main.nf b/target/nextflow/mapping/multi_star/main.nf index d2f165d1..3c905a83 100644 --- a/target/nextflow/mapping/multi_star/main.nf +++ b/target/nextflow/mapping/multi_star/main.nf @@ -1,4 +1,4 @@ -// multi_star v4.0.1 +// multi_star v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "multi_star", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -6382,7 +6382,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -6443,12 +6443,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/multi_star", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -6473,7 +6473,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -7554,7 +7554,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/multi_star", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/multi_star/nextflow.config b/target/nextflow/mapping/multi_star/nextflow.config index 28aba388..f7467a5c 100644 --- a/target/nextflow/mapping/multi_star/nextflow.config +++ b/target/nextflow/mapping/multi_star/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/multi_star' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Align fastq files using STAR.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml index 96e4dc27..87554e98 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/mapping/multi_star_to_h5mu/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "multi_star_to_h5mu" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -177,7 +177,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -206,11 +206,11 @@ build_info: output: "target/nextflow/mapping/multi_star_to_h5mu" executable: "target/nextflow/mapping/multi_star_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -240,7 +240,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/multi_star_to_h5mu/main.nf b/target/nextflow/mapping/multi_star_to_h5mu/main.nf index eb9396c8..baa7b71f 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/main.nf +++ b/target/nextflow/mapping/multi_star_to_h5mu/main.nf @@ -1,4 +1,4 @@ -// multi_star_to_h5mu v4.0.1 +// multi_star_to_h5mu v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "multi_star_to_h5mu", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3268,7 +3268,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3304,12 +3304,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/multi_star_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3334,7 +3334,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3848,7 +3848,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/multi_star_to_h5mu", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config b/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config index 67dc8e43..7e61abea 100644 --- a/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config +++ b/target/nextflow/mapping/multi_star_to_h5mu/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/multi_star_to_h5mu' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert the output of `multi_star` to a h5mu.\n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml index c01ca643..fa51d9ef 100644 --- a/target/nextflow/mapping/samtools_sort/.config.vsh.yaml +++ b/target/nextflow/mapping/samtools_sort/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "samtools_sort" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -258,7 +258,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -282,11 +282,11 @@ build_info: output: "target/nextflow/mapping/samtools_sort" executable: "target/nextflow/mapping/samtools_sort/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -316,7 +316,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/samtools_sort/main.nf b/target/nextflow/mapping/samtools_sort/main.nf index fff14ae9..24799fd4 100644 --- a/target/nextflow/mapping/samtools_sort/main.nf +++ b/target/nextflow/mapping/samtools_sort/main.nf @@ -1,4 +1,4 @@ -// samtools_sort v4.0.1 +// samtools_sort v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "samtools_sort", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3368,7 +3368,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3400,12 +3400,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/samtools_sort", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3430,7 +3430,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3947,7 +3947,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/samtools_sort", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/samtools_sort/nextflow.config b/target/nextflow/mapping/samtools_sort/nextflow.config index 75e03634..f3862679 100644 --- a/target/nextflow/mapping/samtools_sort/nextflow.config +++ b/target/nextflow/mapping/samtools_sort/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/samtools_sort' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Sort and (optionally) index alignments.\n\nReads are sorted by leftmost coordinates, or by read name when `--sort_by_read_names` is used.\n\nAn appropriate `@HD-SO` sort order header tag will be added or an existing one updated if necessary.\n\nNote that to generate an index file (by specifying `--output_bai`), the default coordinate sort must be used.\nThus the `--sort_by_read_names` and `--sort_by ` options are incompatible with `--output_bai`. \n' author = 'Robrecht Cannoodt, Angela Oliveira Pisco' } diff --git a/target/nextflow/mapping/star_align/.config.vsh.yaml b/target/nextflow/mapping/star_align/.config.vsh.yaml index a568592a..a1928832 100644 --- a/target/nextflow/mapping/star_align/.config.vsh.yaml +++ b/target/nextflow/mapping/star_align/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2341,7 +2341,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -2371,11 +2371,11 @@ build_info: output: "target/nextflow/mapping/star_align" executable: "target/nextflow/mapping/star_align/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -2405,7 +2405,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/star_align/main.nf b/target/nextflow/mapping/star_align/main.nf index 18a7afcb..613a0148 100644 --- a/target/nextflow/mapping/star_align/main.nf +++ b/target/nextflow/mapping/star_align/main.nf @@ -1,4 +1,4 @@ -// star_align v4.0.1 +// star_align v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "star_align", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -5466,7 +5466,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -5502,12 +5502,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/star_align", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -5532,7 +5532,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -6340,7 +6340,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/star_align", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/star_align/nextflow.config b/target/nextflow/mapping/star_align/nextflow.config index bf0870f5..1fa8f243 100644 --- a/target/nextflow/mapping/star_align/nextflow.config +++ b/target/nextflow/mapping/star_align/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/star_align' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Align fastq files using STAR.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml index 4cd8fd57..0cbd271e 100644 --- a/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml +++ b/target/nextflow/mapping/star_align_v273a/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "star_align_v273a" namespace: "mapping" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -2341,7 +2341,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -2371,11 +2371,11 @@ build_info: output: "target/nextflow/mapping/star_align_v273a" executable: "target/nextflow/mapping/star_align_v273a/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -2405,7 +2405,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/mapping/star_align_v273a/main.nf b/target/nextflow/mapping/star_align_v273a/main.nf index 95e497b6..c878da55 100644 --- a/target/nextflow/mapping/star_align_v273a/main.nf +++ b/target/nextflow/mapping/star_align_v273a/main.nf @@ -1,4 +1,4 @@ -// star_align_v273a v4.0.1 +// star_align_v273a v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "star_align_v273a", "namespace" : "mapping", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -5466,7 +5466,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -5502,12 +5502,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/star_align_v273a", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -5532,7 +5532,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -6340,7 +6340,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/mapping/star_align_v273a", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/mapping/star_align_v273a/nextflow.config b/target/nextflow/mapping/star_align_v273a/nextflow.config index 1ca0246c..c8a38ce8 100644 --- a/target/nextflow/mapping/star_align_v273a/nextflow.config +++ b/target/nextflow/mapping/star_align_v273a/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'mapping/star_align_v273a' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Align fastq files using STAR.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/metadata/add_id/.config.vsh.yaml b/target/nextflow/metadata/add_id/.config.vsh.yaml index 64ad0207..19b5bf39 100644 --- a/target/nextflow/metadata/add_id/.config.vsh.yaml +++ b/target/nextflow/metadata/add_id/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "add_id" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -185,7 +185,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -226,11 +226,11 @@ build_info: output: "target/nextflow/metadata/add_id" executable: "target/nextflow/metadata/add_id/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -260,7 +260,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/metadata/add_id/main.nf b/target/nextflow/metadata/add_id/main.nf index f994ca25..7b086f07 100644 --- a/target/nextflow/metadata/add_id/main.nf +++ b/target/nextflow/metadata/add_id/main.nf @@ -1,4 +1,4 @@ -// add_id v4.0.1 +// add_id v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "add_id", "namespace" : "metadata", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3269,7 +3269,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3325,12 +3325,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/metadata/add_id", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3355,7 +3355,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3871,7 +3871,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/metadata/add_id", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/metadata/add_id/nextflow.config b/target/nextflow/metadata/add_id/nextflow.config index 856076a4..3360141f 100644 --- a/target/nextflow/metadata/add_id/nextflow.config +++ b/target/nextflow/metadata/add_id/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/add_id' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Add id of .obs. Also allows to make .obs_names (the .obs index) unique \nby prefixing the values with an unique id per .h5mu file.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml index dc167c40..3f828b25 100644 --- a/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/nextflow/metadata/grep_annotation_column/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "grep_annotation_column" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -241,7 +241,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -282,11 +282,11 @@ build_info: output: "target/nextflow/metadata/grep_annotation_column" executable: "target/nextflow/metadata/grep_annotation_column/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -316,7 +316,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/metadata/grep_annotation_column/main.nf b/target/nextflow/metadata/grep_annotation_column/main.nf index c0692094..c22fa532 100644 --- a/target/nextflow/metadata/grep_annotation_column/main.nf +++ b/target/nextflow/metadata/grep_annotation_column/main.nf @@ -1,4 +1,4 @@ -// grep_annotation_column v4.0.1 +// grep_annotation_column v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "grep_annotation_column", "namespace" : "metadata", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3335,7 +3335,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3391,12 +3391,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/metadata/grep_annotation_column", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3421,7 +3421,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4010,7 +4010,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/metadata/grep_annotation_column", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/metadata/grep_annotation_column/nextflow.config b/target/nextflow/metadata/grep_annotation_column/nextflow.config index 1d30120f..08372d4e 100644 --- a/target/nextflow/metadata/grep_annotation_column/nextflow.config +++ b/target/nextflow/metadata/grep_annotation_column/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/grep_annotation_column' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Perform a regex lookup on a column from the annotation matrices .obs or .var.\nThe annotation matrix can originate from either a modality, or all modalities (global .var or .obs).\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/join_csv/.config.vsh.yaml b/target/nextflow/metadata/join_csv/.config.vsh.yaml index f060e75b..1d486dc0 100644 --- a/target/nextflow/metadata/join_csv/.config.vsh.yaml +++ b/target/nextflow/metadata/join_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "join_csv" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -216,7 +216,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -257,11 +257,11 @@ build_info: output: "target/nextflow/metadata/join_csv" executable: "target/nextflow/metadata/join_csv/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -291,7 +291,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/metadata/join_csv/main.nf b/target/nextflow/metadata/join_csv/main.nf index 20f153ec..e9592b57 100644 --- a/target/nextflow/metadata/join_csv/main.nf +++ b/target/nextflow/metadata/join_csv/main.nf @@ -1,4 +1,4 @@ -// join_csv v4.0.1 +// join_csv v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "join_csv", "namespace" : "metadata", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3308,7 +3308,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3364,12 +3364,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/metadata/join_csv", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3394,7 +3394,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3887,7 +3887,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/metadata/join_csv", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/metadata/join_csv/nextflow.config b/target/nextflow/metadata/join_csv/nextflow.config index a15f33cc..f66c198b 100644 --- a/target/nextflow/metadata/join_csv/nextflow.config +++ b/target/nextflow/metadata/join_csv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/join_csv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Join a csv containing metadata to the .obs or .var field of a mudata file.' author = 'Dries Schaumont' } diff --git a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml index 00ad736f..0b2b51d6 100644 --- a/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml +++ b/target/nextflow/metadata/join_uns_to_obs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "join_uns_to_obs" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -164,7 +164,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -205,11 +205,11 @@ build_info: output: "target/nextflow/metadata/join_uns_to_obs" executable: "target/nextflow/metadata/join_uns_to_obs/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -239,7 +239,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/metadata/join_uns_to_obs/main.nf b/target/nextflow/metadata/join_uns_to_obs/main.nf index 24591375..f6cf569b 100644 --- a/target/nextflow/metadata/join_uns_to_obs/main.nf +++ b/target/nextflow/metadata/join_uns_to_obs/main.nf @@ -1,4 +1,4 @@ -// join_uns_to_obs v4.0.1 +// join_uns_to_obs v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "join_uns_to_obs", "namespace" : "metadata", - "version" : "v4.0.1", + "version" : "v4.0.2", "argument_groups" : [ { "name" : "Arguments", @@ -3236,7 +3236,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3292,12 +3292,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/metadata/join_uns_to_obs", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3322,7 +3322,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3799,7 +3799,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/metadata/join_uns_to_obs", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/metadata/join_uns_to_obs/nextflow.config b/target/nextflow/metadata/join_uns_to_obs/nextflow.config index 7847e700..cd2a7067 100644 --- a/target/nextflow/metadata/join_uns_to_obs/nextflow.config +++ b/target/nextflow/metadata/join_uns_to_obs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/join_uns_to_obs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Join a data frame of length 1 (1 row index value) in .uns containing metadata to the .obs of a mudata file.' } diff --git a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml index 9a303374..09816996 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_obsm_to_obs" namespace: "metadata" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -183,7 +183,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -224,11 +224,11 @@ build_info: output: "target/nextflow/metadata/move_obsm_to_obs" executable: "target/nextflow/metadata/move_obsm_to_obs/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -258,7 +258,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/metadata/move_obsm_to_obs/main.nf b/target/nextflow/metadata/move_obsm_to_obs/main.nf index c7d9e0be..fa0b5aeb 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/main.nf +++ b/target/nextflow/metadata/move_obsm_to_obs/main.nf @@ -1,4 +1,4 @@ -// move_obsm_to_obs v4.0.1 +// move_obsm_to_obs v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "move_obsm_to_obs", "namespace" : "metadata", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3268,7 +3268,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3324,12 +3324,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/metadata/move_obsm_to_obs", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3354,7 +3354,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3860,7 +3860,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/metadata/move_obsm_to_obs", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/metadata/move_obsm_to_obs/nextflow.config b/target/nextflow/metadata/move_obsm_to_obs/nextflow.config index 8d639c2c..99670d07 100644 --- a/target/nextflow/metadata/move_obsm_to_obs/nextflow.config +++ b/target/nextflow/metadata/move_obsm_to_obs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'metadata/move_obsm_to_obs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Move a matrix from .obsm to .obs. Newly created columns in .obs will \nbe created from the .obsm key suffixed with an underscore and the name of the columns\nof the specified .obsm matrix.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/neighbors/bbknn/.config.vsh.yaml b/target/nextflow/neighbors/bbknn/.config.vsh.yaml index 97a840cd..0d3a8ac8 100644 --- a/target/nextflow/neighbors/bbknn/.config.vsh.yaml +++ b/target/nextflow/neighbors/bbknn/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bbknn" namespace: "neighbors" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -272,7 +272,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -310,11 +310,11 @@ build_info: output: "target/nextflow/neighbors/bbknn" executable: "target/nextflow/neighbors/bbknn/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -344,7 +344,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/neighbors/bbknn/main.nf b/target/nextflow/neighbors/bbknn/main.nf index 72452250..1635ded8 100644 --- a/target/nextflow/neighbors/bbknn/main.nf +++ b/target/nextflow/neighbors/bbknn/main.nf @@ -1,4 +1,4 @@ -// bbknn v4.0.1 +// bbknn v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bbknn", "namespace" : "neighbors", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3367,7 +3367,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3416,12 +3416,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/neighbors/bbknn", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3446,7 +3446,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3929,7 +3929,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/neighbors/bbknn", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/neighbors/bbknn/nextflow.config b/target/nextflow/neighbors/bbknn/nextflow.config index 8b856ddf..5e75a4f8 100644 --- a/target/nextflow/neighbors/bbknn/nextflow.config +++ b/target/nextflow/neighbors/bbknn/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'neighbors/bbknn' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'BBKNN network generation\n' author = 'Dries De Maeyer, Dries Schaumont' } diff --git a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml index 155b39cf..f8e40489 100644 --- a/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/nextflow/neighbors/find_neighbors/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "find_neighbors" namespace: "neighbors" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -296,7 +296,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -338,11 +338,11 @@ build_info: output: "target/nextflow/neighbors/find_neighbors" executable: "target/nextflow/neighbors/find_neighbors/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -372,7 +372,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/neighbors/find_neighbors/main.nf b/target/nextflow/neighbors/find_neighbors/main.nf index 4f4d0bf8..ea56e8e6 100644 --- a/target/nextflow/neighbors/find_neighbors/main.nf +++ b/target/nextflow/neighbors/find_neighbors/main.nf @@ -1,4 +1,4 @@ -// find_neighbors v4.0.1 +// find_neighbors v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "find_neighbors", "namespace" : "neighbors", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3395,7 +3395,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3452,12 +3452,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/neighbors/find_neighbors", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3482,7 +3482,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3983,7 +3983,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/neighbors/find_neighbors", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/neighbors/find_neighbors/nextflow.config b/target/nextflow/neighbors/find_neighbors/nextflow.config index 4cf6f559..e1649312 100644 --- a/target/nextflow/neighbors/find_neighbors/nextflow.config +++ b/target/nextflow/neighbors/find_neighbors/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'neighbors/find_neighbors' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Compute a neighborhood graph of observations [McInnes18].\n\nThe neighbor search efficiency of this heavily relies on UMAP [McInnes18], which also provides a method for estimating connectivities of data points - the connectivity of the manifold (method==\'umap\'). If method==\'gauss\', connectivities are computed according to [Coifman05], in the adaption of [Haghverdi16].\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml index 5a1c2c88..2f0dedf2 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml +++ b/target/nextflow/process_10xh5/filter_10xh5/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "filter_10xh5" namespace: "process_10xh5" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -182,7 +182,7 @@ engines: id: "docker" image: "eddelbuettel/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -226,11 +226,11 @@ build_info: output: "target/nextflow/process_10xh5/filter_10xh5" executable: "target/nextflow/process_10xh5/filter_10xh5/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -260,7 +260,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/process_10xh5/filter_10xh5/main.nf b/target/nextflow/process_10xh5/filter_10xh5/main.nf index 1a02cf2d..f93b899b 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/main.nf +++ b/target/nextflow/process_10xh5/filter_10xh5/main.nf @@ -1,4 +1,4 @@ -// filter_10xh5 v4.0.1 +// filter_10xh5 v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "filter_10xh5", "namespace" : "process_10xh5", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3264,7 +3264,7 @@ meta = [ "id" : "docker", "image" : "eddelbuettel/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3321,12 +3321,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/process_10xh5/filter_10xh5", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3351,7 +3351,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3886,7 +3886,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/process_10xh5/filter_10xh5", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/process_10xh5/filter_10xh5/nextflow.config b/target/nextflow/process_10xh5/filter_10xh5/nextflow.config index f071be72..bcd413b1 100644 --- a/target/nextflow/process_10xh5/filter_10xh5/nextflow.config +++ b/target/nextflow/process_10xh5/filter_10xh5/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'process_10xh5/filter_10xh5' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Filter a 10x h5 dataset.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml b/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml index bd5000c8..2fd497f1 100644 --- a/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml +++ b/target/nextflow/qc/calculate_atac_qc_metrics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "calculate_atac_qc_metrics" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -249,7 +249,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -283,11 +283,11 @@ build_info: output: "target/nextflow/qc/calculate_atac_qc_metrics" executable: "target/nextflow/qc/calculate_atac_qc_metrics/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -317,7 +317,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/qc/calculate_atac_qc_metrics/main.nf b/target/nextflow/qc/calculate_atac_qc_metrics/main.nf index b5a4581c..5a86706b 100644 --- a/target/nextflow/qc/calculate_atac_qc_metrics/main.nf +++ b/target/nextflow/qc/calculate_atac_qc_metrics/main.nf @@ -1,4 +1,4 @@ -// calculate_atac_qc_metrics v4.0.1 +// calculate_atac_qc_metrics v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "calculate_atac_qc_metrics", "namespace" : "qc", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3331,7 +3331,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3377,12 +3377,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qc/calculate_atac_qc_metrics", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3407,7 +3407,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3946,7 +3946,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/qc/calculate_atac_qc_metrics", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config b/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config index 95e0385c..c0542722 100644 --- a/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config +++ b/target/nextflow/qc/calculate_atac_qc_metrics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/calculate_atac_qc_metrics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Add basic ATAC quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nObs metrics (name in this component -> name in scanpy):\n - n_features_per_cell -> n_genes_by_counts\n - total_fragment_counts -> total_counts\n \n' author = 'Vladimir Shitov' } diff --git a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml index 00fd9e51..c889842d 100644 --- a/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "calculate_qc_metrics" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -295,7 +295,7 @@ engines: id: "docker" image: "python:3.11-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -342,11 +342,11 @@ build_info: output: "target/nextflow/qc/calculate_qc_metrics" executable: "target/nextflow/qc/calculate_qc_metrics/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -376,7 +376,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/qc/calculate_qc_metrics/main.nf b/target/nextflow/qc/calculate_qc_metrics/main.nf index b532a6db..16a82613 100644 --- a/target/nextflow/qc/calculate_qc_metrics/main.nf +++ b/target/nextflow/qc/calculate_qc_metrics/main.nf @@ -1,4 +1,4 @@ -// calculate_qc_metrics v4.0.1 +// calculate_qc_metrics v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "calculate_qc_metrics", "namespace" : "qc", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3381,7 +3381,7 @@ meta = [ "id" : "docker", "image" : "python:3.11-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3446,12 +3446,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qc/calculate_qc_metrics", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3476,7 +3476,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4107,7 +4107,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/qc/calculate_qc_metrics", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/qc/calculate_qc_metrics/nextflow.config b/target/nextflow/qc/calculate_qc_metrics/nextflow.config index 3f5d4e0d..ab6a39a3 100644 --- a/target/nextflow/qc/calculate_qc_metrics/nextflow.config +++ b/target/nextflow/qc/calculate_qc_metrics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/calculate_qc_metrics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Add basic quality control metrics to an .h5mu file.\n\nThe metrics are comparable to what scanpy.pp.calculate_qc_metrics output,\nalthough they have slightly different names:\n\nVar metrics (name in this component -> name in scanpy):\n - pct_dropout -> pct_dropout_by_{expr_type}\n - num_nonzero_obs -> n_cells_by_{expr_type}\n - obs_mean -> mean_{expr_type}\n - total_counts -> total_{expr_type}\n\n Obs metrics:\n - num_nonzero_vars -> n_genes_by_{expr_type}\n - pct_{var_qc_metrics} -> pct_{expr_type}_{qc_var}\n - total_counts_{var_qc_metrics} -> total_{expr_type}_{qc_var}\n - pct_of_counts_in_top_{top_n_vars}_vars -> pct_{expr_type}_in_top_{n}_{var_type}\n - total_counts -> total_{expr_type}\n \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/qc/fastqc/.config.vsh.yaml b/target/nextflow/qc/fastqc/.config.vsh.yaml index 550a1dfd..716b1ddb 100644 --- a/target/nextflow/qc/fastqc/.config.vsh.yaml +++ b/target/nextflow/qc/fastqc/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "fastqc" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -158,7 +158,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -176,11 +176,11 @@ build_info: output: "target/nextflow/qc/fastqc" executable: "target/nextflow/qc/fastqc/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -210,7 +210,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/qc/fastqc/main.nf b/target/nextflow/qc/fastqc/main.nf index b3675c03..cc2a0318 100644 --- a/target/nextflow/qc/fastqc/main.nf +++ b/target/nextflow/qc/fastqc/main.nf @@ -1,4 +1,4 @@ -// fastqc v4.0.1 +// fastqc v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "fastqc", "namespace" : "qc", - "version" : "v4.0.1", + "version" : "v4.0.2", "argument_groups" : [ { "name" : "Arguments", @@ -3226,7 +3226,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3249,12 +3249,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qc/fastqc", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3279,7 +3279,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3726,7 +3726,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/qc/fastqc", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowcpu", diff --git a/target/nextflow/qc/fastqc/nextflow.config b/target/nextflow/qc/fastqc/nextflow.config index 142c7c9f..983334f4 100644 --- a/target/nextflow/qc/fastqc/nextflow.config +++ b/target/nextflow/qc/fastqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/fastqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can take one or more files (by means of shell globbing) or a complete directory.\n' } diff --git a/target/nextflow/qc/multiqc/.config.vsh.yaml b/target/nextflow/qc/multiqc/.config.vsh.yaml index 39b3ce94..e5defd3b 100644 --- a/target/nextflow/qc/multiqc/.config.vsh.yaml +++ b/target/nextflow/qc/multiqc/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "multiqc" namespace: "qc" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -133,7 +133,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -162,11 +162,11 @@ build_info: output: "target/nextflow/qc/multiqc" executable: "target/nextflow/qc/multiqc/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -196,7 +196,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/qc/multiqc/main.nf b/target/nextflow/qc/multiqc/main.nf index ec4eb47b..77964298 100644 --- a/target/nextflow/qc/multiqc/main.nf +++ b/target/nextflow/qc/multiqc/main.nf @@ -1,4 +1,4 @@ -// multiqc v4.0.1 +// multiqc v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "multiqc", "namespace" : "qc", - "version" : "v4.0.1", + "version" : "v4.0.2", "argument_groups" : [ { "name" : "Arguments", @@ -3195,7 +3195,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3236,12 +3236,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qc/multiqc", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3266,7 +3266,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3712,7 +3712,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/qc/multiqc", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/qc/multiqc/nextflow.config b/target/nextflow/qc/multiqc/nextflow.config index 62a364dd..e8f1c404 100644 --- a/target/nextflow/qc/multiqc/nextflow.config +++ b/target/nextflow/qc/multiqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qc/multiqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n' } diff --git a/target/nextflow/query/cellxgene_census/.config.vsh.yaml b/target/nextflow/query/cellxgene_census/.config.vsh.yaml index af8b6520..732d48b2 100644 --- a/target/nextflow/query/cellxgene_census/.config.vsh.yaml +++ b/target/nextflow/query/cellxgene_census/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellxgene_census" namespace: "query" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Matthias Beyens" roles: @@ -506,7 +506,7 @@ engines: id: "docker" image: "python:3.11" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -539,11 +539,11 @@ build_info: output: "target/nextflow/query/cellxgene_census" executable: "target/nextflow/query/cellxgene_census/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -573,7 +573,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/query/cellxgene_census/main.nf b/target/nextflow/query/cellxgene_census/main.nf index 26348b5f..96b45dd3 100644 --- a/target/nextflow/query/cellxgene_census/main.nf +++ b/target/nextflow/query/cellxgene_census/main.nf @@ -1,4 +1,4 @@ -// cellxgene_census v4.0.1 +// cellxgene_census v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3038,7 +3038,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellxgene_census", "namespace" : "query", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Matthias Beyens", @@ -3653,7 +3653,7 @@ meta = [ "id" : "docker", "image" : "python:3.11", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3694,12 +3694,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/query/cellxgene_census", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3724,7 +3724,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4355,7 +4355,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/query/cellxgene_census", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/query/cellxgene_census/nextflow.config b/target/nextflow/query/cellxgene_census/nextflow.config index 6972d71e..be66639f 100644 --- a/target/nextflow/query/cellxgene_census/nextflow.config +++ b/target/nextflow/query/cellxgene_census/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'query/cellxgene_census' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Query cells from a CellxGene Census or custom TileDBSoma object.\nAside from fetching the cells\' RNA counts (`.X`), cell metadata\n(`.obs`) and gene metadata (`.var`), this component also fetches\nthe dataset metadata and joins it into the cell metadata.\n' author = 'Matthias Beyens, Dries De Maeyer, Robrecht Cannoodt, Kai Waldrant' } diff --git a/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml b/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml index b6413616..7b548422 100644 --- a/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml +++ b/target/nextflow/query/tiledb_healthcheck/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tiledb_healthcheck" namespace: "query" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -137,7 +137,7 @@ engines: id: "docker" image: "python:3.12" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "python" @@ -162,11 +162,11 @@ build_info: output: "target/nextflow/query/tiledb_healthcheck" executable: "target/nextflow/query/tiledb_healthcheck/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -196,7 +196,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/query/tiledb_healthcheck/main.nf b/target/nextflow/query/tiledb_healthcheck/main.nf index 928c5ec9..4379eec6 100644 --- a/target/nextflow/query/tiledb_healthcheck/main.nf +++ b/target/nextflow/query/tiledb_healthcheck/main.nf @@ -1,4 +1,4 @@ -// tiledb_healthcheck v4.0.1 +// tiledb_healthcheck v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "tiledb_healthcheck", "namespace" : "query", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3211,7 +3211,7 @@ meta = [ "id" : "docker", "image" : "python:3.12", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3245,12 +3245,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/query/tiledb_healthcheck", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3275,7 +3275,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3744,7 +3744,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/query/tiledb_healthcheck", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/query/tiledb_healthcheck/nextflow.config b/target/nextflow/query/tiledb_healthcheck/nextflow.config index acc81269..314489e9 100644 --- a/target/nextflow/query/tiledb_healthcheck/nextflow.config +++ b/target/nextflow/query/tiledb_healthcheck/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'query/tiledb_healthcheck' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Checks if a provided location can be queried as a TileDB-SOMA database.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml index 23da64e6..17a14b4b 100644 --- a/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_bdrhap_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_bdrhap_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -249,7 +249,7 @@ engines: id: "docker" image: "bdgenomics/rhapsody:2.2.1" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -274,11 +274,11 @@ build_info: output: "target/nextflow/reference/build_bdrhap_reference" executable: "target/nextflow/reference/build_bdrhap_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -308,7 +308,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/reference/build_bdrhap_reference/main.nf b/target/nextflow/reference/build_bdrhap_reference/main.nf index df1e9767..50f10556 100644 --- a/target/nextflow/reference/build_bdrhap_reference/main.nf +++ b/target/nextflow/reference/build_bdrhap_reference/main.nf @@ -1,4 +1,4 @@ -// build_bdrhap_reference v4.0.1 +// build_bdrhap_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "build_bdrhap_reference", "namespace" : "reference", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3341,7 +3341,7 @@ meta = [ "id" : "docker", "image" : "bdgenomics/rhapsody:2.2.1", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3374,12 +3374,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/reference/build_bdrhap_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3404,7 +3404,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4009,7 +4009,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/reference/build_bdrhap_reference", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/reference/build_bdrhap_reference/nextflow.config b/target/nextflow/reference/build_bdrhap_reference/nextflow.config index 3a6b4b6d..628145ba 100644 --- a/target/nextflow/reference/build_bdrhap_reference/nextflow.config +++ b/target/nextflow/reference/build_bdrhap_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/build_bdrhap_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'The Reference Files Generator creates an archive containing Genome Index\nand Transcriptome annotation files needed for the BD Rhapsody Sequencing\nAnalysis Pipeline. The app takes as input one or more FASTA and GTF files\nand produces a compressed archive in the form of a tar.gz file. The \narchive contains:\n \n- STAR index\n- Filtered GTF file\n' author = 'Robrecht Cannoodt, Weiwei Schultz' } diff --git a/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml b/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml index 2a15bddb..1b98308a 100644 --- a/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_cellranger_arc_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_cellranger_arc_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -213,7 +213,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger_arc:2.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -246,11 +246,11 @@ build_info: output: "target/nextflow/reference/build_cellranger_arc_reference" executable: "target/nextflow/reference/build_cellranger_arc_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/reference/build_cellranger_arc_reference/main.nf b/target/nextflow/reference/build_cellranger_arc_reference/main.nf index a78c6158..7e0ba8d3 100644 --- a/target/nextflow/reference/build_cellranger_arc_reference/main.nf +++ b/target/nextflow/reference/build_cellranger_arc_reference/main.nf @@ -1,4 +1,4 @@ -// build_cellranger_arc_reference v4.0.1 +// build_cellranger_arc_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "build_cellranger_arc_reference", "namespace" : "reference", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3295,7 +3295,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger_arc:2.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3336,12 +3336,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/reference/build_cellranger_arc_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3366,7 +3366,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3875,7 +3875,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/reference/build_cellranger_arc_reference", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config b/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config index d4eb1d9d..c605c596 100644 --- a/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config +++ b/target/nextflow/reference/build_cellranger_arc_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/build_cellranger_arc_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Build a Cell Ranger-arc and -atac compatible reference folder from user-supplied genome FASTA and gene GTF files. Creates a new folder named after the genome.' author = 'Vladimir Shitov' } diff --git a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml index 3f48d2be..5166908a 100644 --- a/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_cellranger_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_cellranger_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -182,7 +182,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -214,11 +214,11 @@ build_info: output: "target/nextflow/reference/build_cellranger_reference" executable: "target/nextflow/reference/build_cellranger_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -248,7 +248,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/reference/build_cellranger_reference/main.nf b/target/nextflow/reference/build_cellranger_reference/main.nf index 36c75b66..3a77ddfd 100644 --- a/target/nextflow/reference/build_cellranger_reference/main.nf +++ b/target/nextflow/reference/build_cellranger_reference/main.nf @@ -1,4 +1,4 @@ -// build_cellranger_reference v4.0.1 +// build_cellranger_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "build_cellranger_reference", "namespace" : "reference", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3272,7 +3272,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger:9.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3310,12 +3310,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/reference/build_cellranger_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3340,7 +3340,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3809,7 +3809,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/reference/build_cellranger_reference", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/reference/build_cellranger_reference/nextflow.config b/target/nextflow/reference/build_cellranger_reference/nextflow.config index 564e60ef..ddc18df9 100644 --- a/target/nextflow/reference/build_cellranger_reference/nextflow.config +++ b/target/nextflow/reference/build_cellranger_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/build_cellranger_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files. Creates a new folder named after the genome.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/reference/build_star_reference/.config.vsh.yaml b/target/nextflow/reference/build_star_reference/.config.vsh.yaml index cb51e45c..ee4c8a3c 100644 --- a/target/nextflow/reference/build_star_reference/.config.vsh.yaml +++ b/target/nextflow/reference/build_star_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "build_star_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -208,11 +208,11 @@ build_info: output: "target/nextflow/reference/build_star_reference" executable: "target/nextflow/reference/build_star_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -242,7 +242,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/reference/build_star_reference/main.nf b/target/nextflow/reference/build_star_reference/main.nf index 2a837614..cb8ceaf5 100644 --- a/target/nextflow/reference/build_star_reference/main.nf +++ b/target/nextflow/reference/build_star_reference/main.nf @@ -1,4 +1,4 @@ -// build_star_reference v4.0.1 +// build_star_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "build_star_reference", "namespace" : "reference", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3254,7 +3254,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3290,12 +3290,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/reference/build_star_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3320,7 +3320,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3907,7 +3907,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/reference/build_star_reference", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/reference/build_star_reference/nextflow.config b/target/nextflow/reference/build_star_reference/nextflow.config index e468af93..45e33e43 100644 --- a/target/nextflow/reference/build_star_reference/nextflow.config +++ b/target/nextflow/reference/build_star_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/build_star_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Create a reference for STAR from a set of fasta files.' author = 'Dries Schaumont' } diff --git a/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml b/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml index 8fbffb17..c4ae71f6 100644 --- a/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml +++ b/target/nextflow/reference/cellranger_mkgtf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mkgtf" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -152,7 +152,7 @@ engines: id: "docker" image: "ghcr.io/data-intuitive/cellranger:9.0" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -182,11 +182,11 @@ build_info: output: "target/nextflow/reference/cellranger_mkgtf" executable: "target/nextflow/reference/cellranger_mkgtf/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -216,7 +216,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/reference/cellranger_mkgtf/main.nf b/target/nextflow/reference/cellranger_mkgtf/main.nf index b46a7a8e..0a4ea01d 100644 --- a/target/nextflow/reference/cellranger_mkgtf/main.nf +++ b/target/nextflow/reference/cellranger_mkgtf/main.nf @@ -1,4 +1,4 @@ -// cellranger_mkgtf v4.0.1 +// cellranger_mkgtf v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_mkgtf", "namespace" : "reference", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3228,7 +3228,7 @@ meta = [ "id" : "docker", "image" : "ghcr.io/data-intuitive/cellranger:9.0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3270,12 +3270,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/reference/cellranger_mkgtf", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3300,7 +3300,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3773,7 +3773,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/reference/cellranger_mkgtf", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/reference/cellranger_mkgtf/nextflow.config b/target/nextflow/reference/cellranger_mkgtf/nextflow.config index 78275b6c..ba8f3efe 100644 --- a/target/nextflow/reference/cellranger_mkgtf/nextflow.config +++ b/target/nextflow/reference/cellranger_mkgtf/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/cellranger_mkgtf' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Make a GTF file - filter by a specific attribute.' author = 'Jakub Majercik' } diff --git a/target/nextflow/reference/make_reference/.config.vsh.yaml b/target/nextflow/reference/make_reference/.config.vsh.yaml index bd8d02b6..996044c4 100644 --- a/target/nextflow/reference/make_reference/.config.vsh.yaml +++ b/target/nextflow/reference/make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "make_reference" namespace: "reference" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -208,7 +208,7 @@ engines: id: "docker" image: "ubuntu:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -231,11 +231,11 @@ build_info: output: "target/nextflow/reference/make_reference" executable: "target/nextflow/reference/make_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -265,7 +265,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/reference/make_reference/main.nf b/target/nextflow/reference/make_reference/main.nf index a391e9a9..ce1e4bcc 100644 --- a/target/nextflow/reference/make_reference/main.nf +++ b/target/nextflow/reference/make_reference/main.nf @@ -1,4 +1,4 @@ -// make_reference v4.0.1 +// make_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "make_reference", "namespace" : "reference", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3299,7 +3299,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3327,12 +3327,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/reference/make_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3357,7 +3357,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3862,7 +3862,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/reference/make_reference", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/reference/make_reference/nextflow.config b/target/nextflow/reference/make_reference/nextflow.config index fb432a6a..a09dc537 100644 --- a/target/nextflow/reference/make_reference/nextflow.config +++ b/target/nextflow/reference/make_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'reference/make_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Preprocess and build a transcriptome reference.\n\nExample input files are:\n - `genome_fasta`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/GRCh38.primary_assembly.genome.fa.gz\n - `transcriptome_gtf`: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.annotation.gtf.gz\n - `ercc`: https://assets.thermofisher.com/TFS-Assets/LSG/manuals/ERCC92.zip\n' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/report/mermaid/.config.vsh.yaml b/target/nextflow/report/mermaid/.config.vsh.yaml index b6f5925f..ece2fd65 100644 --- a/target/nextflow/report/mermaid/.config.vsh.yaml +++ b/target/nextflow/report/mermaid/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "mermaid" namespace: "report" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -182,7 +182,7 @@ engines: id: "docker" image: "node:20-bullseye" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "javascript" @@ -203,11 +203,11 @@ build_info: output: "target/nextflow/report/mermaid" executable: "target/nextflow/report/mermaid/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -237,7 +237,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/report/mermaid/main.nf b/target/nextflow/report/mermaid/main.nf index 007f9ce7..80ba9902 100644 --- a/target/nextflow/report/mermaid/main.nf +++ b/target/nextflow/report/mermaid/main.nf @@ -1,4 +1,4 @@ -// mermaid v4.0.1 +// mermaid v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "mermaid", "namespace" : "report", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3264,7 +3264,7 @@ meta = [ "id" : "docker", "image" : "node:20-bullseye", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3293,12 +3293,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/report/mermaid", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3323,7 +3323,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3770,7 +3770,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/report/mermaid", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/mermaid/nextflow.config b/target/nextflow/report/mermaid/nextflow.config index 3e2b9a78..d857f5a6 100644 --- a/target/nextflow/report/mermaid/nextflow.config +++ b/target/nextflow/report/mermaid/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'report/mermaid' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Generates a network from mermaid code.\n' author = 'Dries De Maeyer' } diff --git a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml index 8e22ac21..46fbbe6a 100644 --- a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml +++ b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "assert_test_workflow_2_output" namespace: "test_workflows/multiomics/process_samples" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" info: @@ -136,7 +136,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -169,11 +169,11 @@ build_info: output: "target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output" executable: "target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -203,7 +203,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf index 553f8ad9..c734340d 100644 --- a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf +++ b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/main.nf @@ -1,4 +1,4 @@ -// assert_test_workflow_2_output v4.0.1 +// assert_test_workflow_2_output v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "assert_test_workflow_2_output", "namespace" : "test_workflows/multiomics/process_samples", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3208,7 +3208,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3249,12 +3249,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3279,7 +3279,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3974,7 +3974,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/test_workflows/multiomics/process_samples/assert_test_workflow_2_output", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem" diff --git a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config index 09b6dea3..eb71a3bd 100644 --- a/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config +++ b/target/nextflow/test_workflows/multiomics/process_samples/assert_test_workflow_2_output/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'test_workflows/multiomics/process_samples/assert_test_workflow_2_output' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This component tests the output of the integration test of process_samples test_wf.' author = 'Dries Schaumont' } diff --git a/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml b/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml index 2b998860..7f5312d2 100644 --- a/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml +++ b/target/nextflow/transform/bpcells_regress_out/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bpcells_regress_out" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -284,11 +284,11 @@ build_info: output: "target/nextflow/transform/bpcells_regress_out" executable: "target/nextflow/transform/bpcells_regress_out/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -318,7 +318,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/bpcells_regress_out/main.nf b/target/nextflow/transform/bpcells_regress_out/main.nf index c200f54c..47d099fb 100644 --- a/target/nextflow/transform/bpcells_regress_out/main.nf +++ b/target/nextflow/transform/bpcells_regress_out/main.nf @@ -1,4 +1,4 @@ -// bpcells_regress_out v4.0.1 +// bpcells_regress_out v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bpcells_regress_out", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3325,7 +3325,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3408,12 +3408,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/bpcells_regress_out", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3438,7 +3438,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3949,7 +3949,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/bpcells_regress_out", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/transform/bpcells_regress_out/nextflow.config b/target/nextflow/transform/bpcells_regress_out/nextflow.config index b714ced4..dee98c70 100644 --- a/target/nextflow/transform/bpcells_regress_out/nextflow.config +++ b/target/nextflow/transform/bpcells_regress_out/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/bpcells_regress_out' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Regress out the effects of confounding variables using a linear least squares regression model with BPCells.\n' author = 'Dorien Roosen, Robrecht Cannoodt, Weiwei Schultz' } diff --git a/target/nextflow/transform/clr/.config.vsh.yaml b/target/nextflow/transform/clr/.config.vsh.yaml index 373d7513..f3bc6d18 100644 --- a/target/nextflow/transform/clr/.config.vsh.yaml +++ b/target/nextflow/transform/clr/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "clr" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -203,7 +203,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -240,11 +240,11 @@ build_info: output: "target/nextflow/transform/clr" executable: "target/nextflow/transform/clr/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -274,7 +274,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/clr/main.nf b/target/nextflow/transform/clr/main.nf index 58b7f6b0..eff671d9 100644 --- a/target/nextflow/transform/clr/main.nf +++ b/target/nextflow/transform/clr/main.nf @@ -1,4 +1,4 @@ -// clr v4.0.1 +// clr v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "clr", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3289,7 +3289,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3337,12 +3337,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/clr", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3367,7 +3367,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3853,7 +3853,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/clr", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/transform/clr/nextflow.config b/target/nextflow/transform/clr/nextflow.config index 0ba7413a..09cf62fc 100644 --- a/target/nextflow/transform/clr/nextflow.config +++ b/target/nextflow/transform/clr/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/clr' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Perform CLR normalization on CITE-seq data (Stoeckius et al., 2017).\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/transform/delete_layer/.config.vsh.yaml b/target/nextflow/transform/delete_layer/.config.vsh.yaml index 3f4ef187..784cb417 100644 --- a/target/nextflow/transform/delete_layer/.config.vsh.yaml +++ b/target/nextflow/transform/delete_layer/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "delete_layer" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -186,7 +186,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -227,11 +227,11 @@ build_info: output: "target/nextflow/transform/delete_layer" executable: "target/nextflow/transform/delete_layer/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -261,7 +261,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/delete_layer/main.nf b/target/nextflow/transform/delete_layer/main.nf index cce03334..90143663 100644 --- a/target/nextflow/transform/delete_layer/main.nf +++ b/target/nextflow/transform/delete_layer/main.nf @@ -1,4 +1,4 @@ -// delete_layer v4.0.1 +// delete_layer v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "delete_layer", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3273,7 +3273,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3329,12 +3329,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/delete_layer", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3359,7 +3359,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3844,7 +3844,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/delete_layer", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/transform/delete_layer/nextflow.config b/target/nextflow/transform/delete_layer/nextflow.config index b935d697..1506cac2 100644 --- a/target/nextflow/transform/delete_layer/nextflow.config +++ b/target/nextflow/transform/delete_layer/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/delete_layer' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Delete an anndata layer from one or more modalities.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/transform/log1p/.config.vsh.yaml b/target/nextflow/transform/log1p/.config.vsh.yaml index 7bedc491..2684fe85 100644 --- a/target/nextflow/transform/log1p/.config.vsh.yaml +++ b/target/nextflow/transform/log1p/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "log1p" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -217,7 +217,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -253,11 +253,11 @@ build_info: output: "target/nextflow/transform/log1p" executable: "target/nextflow/transform/log1p/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -287,7 +287,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/log1p/main.nf b/target/nextflow/transform/log1p/main.nf index bb74f566..78f335bf 100644 --- a/target/nextflow/transform/log1p/main.nf +++ b/target/nextflow/transform/log1p/main.nf @@ -1,4 +1,4 @@ -// log1p v4.0.1 +// log1p v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "log1p", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3316,7 +3316,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3363,12 +3363,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/log1p", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3393,7 +3393,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3879,7 +3879,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/log1p", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/transform/log1p/nextflow.config b/target/nextflow/transform/log1p/nextflow.config index 33620884..acc78f6d 100644 --- a/target/nextflow/transform/log1p/nextflow.config +++ b/target/nextflow/transform/log1p/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/log1p' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Logarithmize the data matrix. Computes X = log(X + 1), where log denotes the natural logarithm unless a different base is given.\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/transform/move_layer/.config.vsh.yaml b/target/nextflow/transform/move_layer/.config.vsh.yaml index 0215f2dc..e9aacf08 100644 --- a/target/nextflow/transform/move_layer/.config.vsh.yaml +++ b/target/nextflow/transform/move_layer/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "move_layer" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" argument_groups: - name: "Arguments" arguments: @@ -176,7 +176,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -217,11 +217,11 @@ build_info: output: "target/nextflow/transform/move_layer" executable: "target/nextflow/transform/move_layer/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -251,7 +251,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/move_layer/main.nf b/target/nextflow/transform/move_layer/main.nf index 378702d8..105a23f6 100644 --- a/target/nextflow/transform/move_layer/main.nf +++ b/target/nextflow/transform/move_layer/main.nf @@ -1,4 +1,4 @@ -// move_layer v4.0.1 +// move_layer v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "move_layer", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "argument_groups" : [ { "name" : "Arguments", @@ -3245,7 +3245,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3301,12 +3301,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/move_layer", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3331,7 +3331,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3818,7 +3818,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/move_layer", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "singlecpu", diff --git a/target/nextflow/transform/move_layer/nextflow.config b/target/nextflow/transform/move_layer/nextflow.config index 2d8f85bb..a1a608b3 100644 --- a/target/nextflow/transform/move_layer/nextflow.config +++ b/target/nextflow/transform/move_layer/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/move_layer' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Move a data matrix stored at the .layers or .X attributes in a MuData object to another layer.' } diff --git a/target/nextflow/transform/normalize_total/.config.vsh.yaml b/target/nextflow/transform/normalize_total/.config.vsh.yaml index 61aa3c99..6d7e887f 100644 --- a/target/nextflow/transform/normalize_total/.config.vsh.yaml +++ b/target/nextflow/transform/normalize_total/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "normalize_total" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -229,7 +229,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -271,11 +271,11 @@ build_info: output: "target/nextflow/transform/normalize_total" executable: "target/nextflow/transform/normalize_total/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -305,7 +305,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/normalize_total/main.nf b/target/nextflow/transform/normalize_total/main.nf index 2c519bb2..c1d9e98a 100644 --- a/target/nextflow/transform/normalize_total/main.nf +++ b/target/nextflow/transform/normalize_total/main.nf @@ -1,4 +1,4 @@ -// normalize_total v4.0.1 +// normalize_total v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "normalize_total", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3319,7 +3319,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3376,12 +3376,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/normalize_total", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3406,7 +3406,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3896,7 +3896,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/normalize_total", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/transform/normalize_total/nextflow.config b/target/nextflow/transform/normalize_total/nextflow.config index b13f6a51..cd3f7e8a 100644 --- a/target/nextflow/transform/normalize_total/nextflow.config +++ b/target/nextflow/transform/normalize_total/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/normalize_total' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Normalize counts per cell.\n\nNormalize each cell by total counts over all genes, so that every cell has the same total count after normalization. If choosing target_sum=1e6, this is CPM normalization.\n\nIf exclude_highly_expressed=True, very highly expressed genes are excluded from the computation of the normalization factor (size factor) for each cell. This is meaningful as these can strongly influence the resulting normalized values for all other genes [Weinreb17].\n' author = 'Dries De Maeyer, Robrecht Cannoodt' } diff --git a/target/nextflow/transform/regress_out/.config.vsh.yaml b/target/nextflow/transform/regress_out/.config.vsh.yaml index 651f16ad..364b1248 100644 --- a/target/nextflow/transform/regress_out/.config.vsh.yaml +++ b/target/nextflow/transform/regress_out/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "regress_out" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -206,7 +206,7 @@ engines: id: "docker" image: "python:3.13-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -248,11 +248,11 @@ build_info: output: "target/nextflow/transform/regress_out" executable: "target/nextflow/transform/regress_out/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -282,7 +282,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/regress_out/main.nf b/target/nextflow/transform/regress_out/main.nf index f57dfc16..f9835ce8 100644 --- a/target/nextflow/transform/regress_out/main.nf +++ b/target/nextflow/transform/regress_out/main.nf @@ -1,4 +1,4 @@ -// regress_out v4.0.1 +// regress_out v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "regress_out", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3290,7 +3290,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3347,12 +3347,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/regress_out", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3377,7 +3377,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3861,7 +3861,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/regress_out", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/transform/regress_out/nextflow.config b/target/nextflow/transform/regress_out/nextflow.config index 4fd778e4..e54dbf75 100644 --- a/target/nextflow/transform/regress_out/nextflow.config +++ b/target/nextflow/transform/regress_out/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/regress_out' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Regress out (mostly) unwanted sources of variation.\nUses simple linear regression. This is inspired by Seurat\'s regressOut function in R [Satija15]. \nNote that this function tends to overcorrect in certain circumstances as described in issue theislab/scanpy#526.\nSee https://github.com/theislab/scanpy/issues/526.\n' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/transform/scale/.config.vsh.yaml b/target/nextflow/transform/scale/.config.vsh.yaml index 72fcb896..277f9c16 100644 --- a/target/nextflow/transform/scale/.config.vsh.yaml +++ b/target/nextflow/transform/scale/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scale" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -204,7 +204,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -246,11 +246,11 @@ build_info: output: "target/nextflow/transform/scale" executable: "target/nextflow/transform/scale/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/scale/main.nf b/target/nextflow/transform/scale/main.nf index 50a741c5..4c62e9ec 100644 --- a/target/nextflow/transform/scale/main.nf +++ b/target/nextflow/transform/scale/main.nf @@ -1,4 +1,4 @@ -// scale v4.0.1 +// scale v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scale", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3291,7 +3291,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3348,12 +3348,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/scale", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3378,7 +3378,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3873,7 +3873,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/scale", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "lowmem", diff --git a/target/nextflow/transform/scale/nextflow.config b/target/nextflow/transform/scale/nextflow.config index b011135d..8c0caa75 100644 --- a/target/nextflow/transform/scale/nextflow.config +++ b/target/nextflow/transform/scale/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/scale' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Scale data to unit variance and zero mean.\n' author = 'Dries Schaumont' } diff --git a/target/nextflow/transform/tfidf/.config.vsh.yaml b/target/nextflow/transform/tfidf/.config.vsh.yaml index 5178f4ab..1e6c18da 100644 --- a/target/nextflow/transform/tfidf/.config.vsh.yaml +++ b/target/nextflow/transform/tfidf/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "tfidf" namespace: "transform" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Vladimir Shitov" roles: @@ -237,7 +237,7 @@ engines: id: "docker" image: "python:3.13-slim-bullseye" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -277,11 +277,11 @@ build_info: output: "target/nextflow/transform/tfidf" executable: "target/nextflow/transform/tfidf/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -311,7 +311,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/transform/tfidf/main.nf b/target/nextflow/transform/tfidf/main.nf index 8c6873d3..c97a96f2 100644 --- a/target/nextflow/transform/tfidf/main.nf +++ b/target/nextflow/transform/tfidf/main.nf @@ -1,4 +1,4 @@ -// tfidf v4.0.1 +// tfidf v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "tfidf", "namespace" : "transform", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Vladimir Shitov", @@ -3325,7 +3325,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-slim-bullseye", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3376,12 +3376,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/transform/tfidf", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3406,7 +3406,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3892,7 +3892,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/transform/tfidf", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "midmem", diff --git a/target/nextflow/transform/tfidf/nextflow.config b/target/nextflow/transform/tfidf/nextflow.config index d35ffe42..37b9bf53 100644 --- a/target/nextflow/transform/tfidf/nextflow.config +++ b/target/nextflow/transform/tfidf/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'transform/tfidf' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Perform TF-IDF normalization of the data (typically, ATAC).\n\nTF-IDF stands for "term frequency - inverse document frequency". It is a technique from natural language processing analysis.\nIn the context of ATAC data, "terms" are the features (genes) and "documents" are the observations (cells). \nTF-IDF normalization is applied to single-cell ATAC-seq data to highlight the importance of specific genomic regions (typically peaks)\nacross different cells while down-weighting regions that are commonly accessible across many cells. \n' author = 'Vladimir Shitov' } diff --git a/target/nextflow/velocity/scvelo/.config.vsh.yaml b/target/nextflow/velocity/scvelo/.config.vsh.yaml index c0b98439..8ea9c1a7 100644 --- a/target/nextflow/velocity/scvelo/.config.vsh.yaml +++ b/target/nextflow/velocity/scvelo/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvelo" namespace: "velocity" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -311,7 +311,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "apt" @@ -356,11 +356,11 @@ build_info: output: "target/nextflow/velocity/scvelo" executable: "target/nextflow/velocity/scvelo/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -390,7 +390,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/velocity/scvelo/main.nf b/target/nextflow/velocity/scvelo/main.nf index 396e9a1a..33349a72 100644 --- a/target/nextflow/velocity/scvelo/main.nf +++ b/target/nextflow/velocity/scvelo/main.nf @@ -1,4 +1,4 @@ -// scvelo v4.0.1 +// scvelo v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scvelo", "namespace" : "velocity", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3411,7 +3411,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3471,12 +3471,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/velocity/scvelo", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3501,7 +3501,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -4111,7 +4111,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/velocity/scvelo", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/velocity/scvelo/nextflow.config b/target/nextflow/velocity/scvelo/nextflow.config index 564338f8..2b683e64 100644 --- a/target/nextflow/velocity/scvelo/nextflow.config +++ b/target/nextflow/velocity/scvelo/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'velocity/scvelo' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' author = 'Dries Schaumont' } diff --git a/target/nextflow/velocity/velocyto/.config.vsh.yaml b/target/nextflow/velocity/velocyto/.config.vsh.yaml index 2ac81554..6d430579 100644 --- a/target/nextflow/velocity/velocyto/.config.vsh.yaml +++ b/target/nextflow/velocity/velocyto/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "velocyto" namespace: "velocity" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -202,7 +202,7 @@ engines: id: "docker" image: "python:3.13" target_registry: "images.viash-hub.com" - target_tag: "v4.0.1" + target_tag: "v4.0.2" namespace_separator: "/" setup: - type: "docker" @@ -246,11 +246,11 @@ build_info: output: "target/nextflow/velocity/velocyto" executable: "target/nextflow/velocity/velocyto/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -280,7 +280,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/velocity/velocyto/main.nf b/target/nextflow/velocity/velocyto/main.nf index 4d34d6c3..3ae43425 100644 --- a/target/nextflow/velocity/velocyto/main.nf +++ b/target/nextflow/velocity/velocyto/main.nf @@ -1,4 +1,4 @@ -// velocyto v4.0.1 +// velocyto v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "velocyto", "namespace" : "velocity", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3292,7 +3292,7 @@ meta = [ "id" : "docker", "image" : "python:3.13", "target_registry" : "images.viash-hub.com", - "target_tag" : "v4.0.1", + "target_tag" : "v4.0.2", "namespace_separator" : "/", "setup" : [ { @@ -3355,12 +3355,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/velocity/velocyto", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3385,7 +3385,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", @@ -3864,7 +3864,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/openpipeline/velocity/velocyto", - "tag" : "v4.0.1" + "tag" : "v4.0.2" }, "label" : [ "highmem", diff --git a/target/nextflow/velocity/velocyto/nextflow.config b/target/nextflow/velocity/velocyto/nextflow.config index 96b19188..2b1faeb7 100644 --- a/target/nextflow/velocity/velocyto/nextflow.config +++ b/target/nextflow/velocity/velocyto/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'velocity/velocyto' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Runs the velocity analysis on a BAM file, outputting a loom file.' author = 'Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml b/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml index 38280e97..aef47532 100644 --- a/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml +++ b/target/nextflow/workflows/annotation/celltypist/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "celltypist" namespace: "workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -389,14 +389,14 @@ build_info: output: "target/nextflow/workflows/annotation/celltypist" executable: "target/nextflow/workflows/annotation/celltypist/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/_private/nextflow/workflows/rna/log_normalize" - "target/nextflow/annotate/celltypist" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -426,7 +426,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/annotation/celltypist/main.nf b/target/nextflow/workflows/annotation/celltypist/main.nf index 1a40f9bb..7eaa41d6 100644 --- a/target/nextflow/workflows/annotation/celltypist/main.nf +++ b/target/nextflow/workflows/annotation/celltypist/main.nf @@ -1,4 +1,4 @@ -// celltypist v4.0.1 +// celltypist v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "celltypist", "namespace" : "workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3517,12 +3517,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/celltypist", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3547,7 +3547,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/annotation/celltypist/nextflow.config b/target/nextflow/workflows/annotation/celltypist/nextflow.config index 27fd9d55..9dce2e14 100644 --- a/target/nextflow/workflows/annotation/celltypist/nextflow.config +++ b/target/nextflow/workflows/annotation/celltypist/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/annotation/celltypist' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Cell type annotation workflow by performing lognormalization of the raw counts layer followed by cell type annotation with CellTypist.' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml b/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml index 4680cfed..3e86a0cd 100644 --- a/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml +++ b/target/nextflow/workflows/annotation/harmony_knn/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "harmony_knn" namespace: "workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -444,7 +444,7 @@ build_info: output: "target/nextflow/workflows/annotation/harmony_knn" executable: "target/nextflow/workflows/annotation/harmony_knn/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/workflows/integration/harmony_leiden" @@ -459,7 +459,7 @@ build_info: - "target/nextflow/dataflow/merge" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -489,7 +489,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/annotation/harmony_knn/main.nf b/target/nextflow/workflows/annotation/harmony_knn/main.nf index fcafb425..2f9b8a9b 100644 --- a/target/nextflow/workflows/annotation/harmony_knn/main.nf +++ b/target/nextflow/workflows/annotation/harmony_knn/main.nf @@ -1,4 +1,4 @@ -// harmony_knn v4.0.1 +// harmony_knn v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "harmony_knn", "namespace" : "workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3596,12 +3596,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/harmony_knn", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3626,7 +3626,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/annotation/harmony_knn/nextflow.config b/target/nextflow/workflows/annotation/harmony_knn/nextflow.config index 18380958..7635d545 100644 --- a/target/nextflow/workflows/annotation/harmony_knn/nextflow.config +++ b/target/nextflow/workflows/annotation/harmony_knn/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/annotation/harmony_knn' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Cell type annotation workflow by performing harmony integration of reference and query dataset followed by KNN label transfer.' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml b/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml index de770d66..be6665fb 100644 --- a/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml +++ b/target/nextflow/workflows/annotation/scanvi_scarches/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanvi_scarches" namespace: "workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -558,7 +558,7 @@ build_info: output: "target/nextflow/workflows/annotation/scanvi_scarches" executable: "target/nextflow/workflows/annotation/scanvi_scarches/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/integrate/scvi" @@ -567,7 +567,7 @@ build_info: - "target/nextflow/workflows/multiomics/neighbors_leiden_umap" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -597,7 +597,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/annotation/scanvi_scarches/main.nf b/target/nextflow/workflows/annotation/scanvi_scarches/main.nf index 8b9a67ab..18380588 100644 --- a/target/nextflow/workflows/annotation/scanvi_scarches/main.nf +++ b/target/nextflow/workflows/annotation/scanvi_scarches/main.nf @@ -1,4 +1,4 @@ -// scanvi_scarches v4.0.1 +// scanvi_scarches v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scanvi_scarches", "namespace" : "workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3687,12 +3687,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/scanvi_scarches", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3717,7 +3717,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config b/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config index 712485b1..1ddf75b8 100644 --- a/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config +++ b/target/nextflow/workflows/annotation/scanvi_scarches/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/annotation/scanvi_scarches' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Cell type annotation workflow using ScanVI with scArches for reference mapping.' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml b/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml index f856b572..d5f0d620 100644 --- a/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml +++ b/target/nextflow/workflows/annotation/scvi_knn/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvi_knn" namespace: "workflows/annotation" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -530,7 +530,7 @@ build_info: output: "target/nextflow/workflows/annotation/scvi_knn" executable: "target/nextflow/workflows/annotation/scvi_knn/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/workflows/integration/scvi_leiden" @@ -544,7 +544,7 @@ build_info: - "target/nextflow/dataflow/merge" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -574,7 +574,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/annotation/scvi_knn/main.nf b/target/nextflow/workflows/annotation/scvi_knn/main.nf index 9d945fc6..0fa18a10 100644 --- a/target/nextflow/workflows/annotation/scvi_knn/main.nf +++ b/target/nextflow/workflows/annotation/scvi_knn/main.nf @@ -1,4 +1,4 @@ -// scvi_knn v4.0.1 +// scvi_knn v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scvi_knn", "namespace" : "workflows/annotation", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3689,12 +3689,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/annotation/scvi_knn", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3719,7 +3719,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/annotation/scvi_knn/nextflow.config b/target/nextflow/workflows/annotation/scvi_knn/nextflow.config index 5d439777..d9b827fc 100644 --- a/target/nextflow/workflows/annotation/scvi_knn/nextflow.config +++ b/target/nextflow/workflows/annotation/scvi_knn/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/annotation/scvi_knn' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = '"Cell type annotation workflow that performs scVI integration of reference and query dataset followed by KNN label transfer. \nThe query and reference datasets are expected to be pre-processed in the same way, for example with the `process_samples` workflow of OpenPipeline.\nNote that this workflow will integrate the reference dataset from scratch and integrate the query dataset in the same embedding space. \nThe workflow does not currently output the trained SCVI reference model."\n' author = 'Dorien Roosen, Weiwei Schultz' } diff --git a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml index 8e03ea31..8f5f9ad2 100644 --- a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml +++ b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pseudobulk_deseq2" namespace: "workflows/differential_expression" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Jakub Majercik" roles: @@ -363,7 +363,7 @@ build_info: output: "target/nextflow/workflows/differential_expression/pseudobulk_deseq2" executable: "target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/differential_expression/create_pseudobulk" @@ -374,7 +374,7 @@ build_info: - "target/nextflow/filter/do_filter" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -404,7 +404,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf index d27bf294..0e11794c 100644 --- a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf +++ b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/main.nf @@ -1,4 +1,4 @@ -// pseudobulk_deseq2 v4.0.1 +// pseudobulk_deseq2 v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "pseudobulk_deseq2", "namespace" : "workflows/differential_expression", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Jakub Majercik", @@ -3495,12 +3495,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/differential_expression/pseudobulk_deseq2", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3525,7 +3525,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config index b5154f67..1e63dbc5 100644 --- a/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config +++ b/target/nextflow/workflows/differential_expression/pseudobulk_deseq2/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/differential_expression/pseudobulk_deseq2' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs pseudobulk generation and subsequent differential expression analysis using DESeq2.\n' author = 'Jakub Majercik, Weiwei Schultz' } diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml b/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml index 23fb8d47..be29f88a 100644 --- a/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml +++ b/target/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "gdo_singlesample" namespace: "workflows/gdo" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -225,14 +225,14 @@ build_info: output: "target/nextflow/workflows/gdo/gdo_singlesample" executable: "target/nextflow/workflows/gdo/gdo_singlesample/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/filter/filter_with_counts" - "target/nextflow/filter/do_filter" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -262,7 +262,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/main.nf b/target/nextflow/workflows/gdo/gdo_singlesample/main.nf index 6b1a40d6..f8b4b24c 100644 --- a/target/nextflow/workflows/gdo/gdo_singlesample/main.nf +++ b/target/nextflow/workflows/gdo/gdo_singlesample/main.nf @@ -1,4 +1,4 @@ -// gdo_singlesample v4.0.1 +// gdo_singlesample v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "gdo_singlesample", "namespace" : "workflows/gdo", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3327,12 +3327,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/gdo/gdo_singlesample", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3357,7 +3357,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config b/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config index 748fcab5..5979bd8d 100644 --- a/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config +++ b/target/nextflow/workflows/gdo/gdo_singlesample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/gdo/gdo_singlesample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Processing unimodal single-sample guide-derived oligonucleotide (GDO) data.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml b/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml index 5140c331..26b62ca0 100644 --- a/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/bd_rhapsody/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bd_rhapsody" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Robrecht Cannoodt" roles: @@ -609,14 +609,14 @@ build_info: output: "target/nextflow/workflows/ingestion/bd_rhapsody" executable: "target/nextflow/workflows/ingestion/bd_rhapsody/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/mapping/bd_rhapsody" - "target/nextflow/convert/from_bdrhap_to_h5mu" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -646,7 +646,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf b/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf index 0c19764d..1b4e81e9 100644 --- a/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf +++ b/target/nextflow/workflows/ingestion/bd_rhapsody/main.nf @@ -1,4 +1,4 @@ -// bd_rhapsody v4.0.1 +// bd_rhapsody v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bd_rhapsody", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Robrecht Cannoodt", @@ -3775,12 +3775,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/bd_rhapsody", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3805,7 +3805,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config b/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config index 15b7dc2b..08aa0ea8 100644 --- a/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config +++ b/target/nextflow/workflows/ingestion/bd_rhapsody/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/bd_rhapsody' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'BD Rhapsody Sequence Analysis CWL pipeline v2.2.1\n\nThis pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported\nsequencing libraries are those generated by the BD Rhapsody assay kits, including: Whole Transcriptome\nmRNA, Targeted mRNA, AbSeq Antibody-Oligonucleotides, Single-Cell Multiplexing, TCR/BCR, and\nATAC-Seq\n\nThe CWL pipeline file is obtained by cloning \'https://bitbucket.org/CRSwDev/cwl\' and removing all objects with class \'DockerRequirement\' from the YAML.\n' author = 'Robrecht Cannoodt, Dorien Roosen' } diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml index 04951cd2..09161b0f 100644 --- a/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/cellranger_mapping/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_mapping" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -324,7 +324,7 @@ build_info: output: "target/nextflow/workflows/ingestion/cellranger_mapping" executable: "target/nextflow/workflows/ingestion/cellranger_mapping/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/mapping/cellranger_count" @@ -332,7 +332,7 @@ build_info: - "target/nextflow/convert/from_10xh5_to_h5mu" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -362,7 +362,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf b/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf index b5d43e93..d517b9e1 100644 --- a/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf +++ b/target/nextflow/workflows/ingestion/cellranger_mapping/main.nf @@ -1,4 +1,4 @@ -// cellranger_mapping v4.0.1 +// cellranger_mapping v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_mapping", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3455,12 +3455,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/cellranger_mapping", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3485,7 +3485,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config index 490b3756..044886f9 100644 --- a/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config +++ b/target/nextflow/workflows/ingestion/cellranger_mapping/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/cellranger_mapping' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A pipeline for running Cell Ranger mapping.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt, Dries De Maeyer' } diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml index f3d81c77..c0a9e316 100644 --- a/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/cellranger_multi/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_multi" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -907,14 +907,14 @@ build_info: output: "target/nextflow/workflows/ingestion/cellranger_multi" executable: "target/nextflow/workflows/ingestion/cellranger_multi/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/mapping/cellranger_multi" - "target/nextflow/convert/from_cellranger_multi_to_h5mu" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -944,7 +944,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/main.nf b/target/nextflow/workflows/ingestion/cellranger_multi/main.nf index a7d8169a..c51e969c 100644 --- a/target/nextflow/workflows/ingestion/cellranger_multi/main.nf +++ b/target/nextflow/workflows/ingestion/cellranger_multi/main.nf @@ -1,4 +1,4 @@ -// cellranger_multi v4.0.1 +// cellranger_multi v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_multi", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3993,12 +3993,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/cellranger_multi", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -4023,7 +4023,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config index 7f78e952..4a797558 100644 --- a/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config +++ b/target/nextflow/workflows/ingestion/cellranger_multi/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/cellranger_multi' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A pipeline for running Cell Ranger multi.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml b/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml index 225315b5..274c635b 100644 --- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "cellranger_postprocessing" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -234,7 +234,7 @@ build_info: output: "target/nextflow/workflows/ingestion/cellranger_postprocessing" executable: "target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/correction/cellbender_remove_background" @@ -242,7 +242,7 @@ build_info: - "target/nextflow/filter/subset_h5mu" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -272,7 +272,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf b/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf index 040a3ee9..67abc780 100644 --- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf +++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/main.nf @@ -1,4 +1,4 @@ -// cellranger_postprocessing v4.0.1 +// cellranger_postprocessing v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "cellranger_postprocessing", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3357,12 +3357,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/cellranger_postprocessing", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3387,7 +3387,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config b/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config index 371a12d1..f70a5456 100644 --- a/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config +++ b/target/nextflow/workflows/ingestion/cellranger_postprocessing/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/cellranger_postprocessing' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Post-processing Cell Ranger datasets.' author = 'Angela Oliveira Pisco, Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml b/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml index a9f17c02..0c97b89c 100644 --- a/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/conversion/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "conversion" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -210,7 +210,7 @@ build_info: output: "target/nextflow/workflows/ingestion/conversion" executable: "target/nextflow/workflows/ingestion/conversion/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/convert/from_10xh5_to_h5mu" @@ -218,7 +218,7 @@ build_info: - "target/nextflow/convert/from_h5ad_to_h5mu" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -248,7 +248,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/conversion/main.nf b/target/nextflow/workflows/ingestion/conversion/main.nf index e2ceac3b..d275099e 100644 --- a/target/nextflow/workflows/ingestion/conversion/main.nf +++ b/target/nextflow/workflows/ingestion/conversion/main.nf @@ -1,4 +1,4 @@ -// conversion v4.0.1 +// conversion v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "conversion", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3322,12 +3322,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/conversion", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3352,7 +3352,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/conversion/nextflow.config b/target/nextflow/workflows/ingestion/conversion/nextflow.config index a31d4379..65099d3b 100644 --- a/target/nextflow/workflows/ingestion/conversion/nextflow.config +++ b/target/nextflow/workflows/ingestion/conversion/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/conversion' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A pipeline to convert different file formats to .h5mu.' author = 'Dries Schaumont, Dries De Maeyer' } diff --git a/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml b/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml index 52dd22a2..25dfdea9 100644 --- a/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/demux/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "demux" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Toni Verbeiren" roles: @@ -293,7 +293,7 @@ build_info: output: "target/nextflow/workflows/ingestion/demux" executable: "target/nextflow/workflows/ingestion/demux/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/demux/cellranger_mkfastq" @@ -303,7 +303,7 @@ build_info: - "target/nextflow/qc/multiqc" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -333,7 +333,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/demux/main.nf b/target/nextflow/workflows/ingestion/demux/main.nf index 9961c73b..1296cb74 100644 --- a/target/nextflow/workflows/ingestion/demux/main.nf +++ b/target/nextflow/workflows/ingestion/demux/main.nf @@ -1,4 +1,4 @@ -// demux v4.0.1 +// demux v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3039,7 +3039,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "demux", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Toni Verbeiren", @@ -3438,12 +3438,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/demux", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3468,7 +3468,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/demux/nextflow.config b/target/nextflow/workflows/ingestion/demux/nextflow.config index 9ccd47ed..d2c48ee3 100644 --- a/target/nextflow/workflows/ingestion/demux/nextflow.config +++ b/target/nextflow/workflows/ingestion/demux/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/demux' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Convert `.bcl` files to `.fastq` files using bcl2fastq, bcl-convert or Cell Ranger mkfastq.\n' author = 'Toni Verbeiren, Marijke Van Moerbeke, Angela Oliveira Pisco, Samuel D\'Souza, Robrecht Cannoodt' } diff --git a/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml b/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml index e3ad98bd..0ea5c18e 100644 --- a/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/make_reference/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "make_reference" namespace: "workflows/ingestion" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Angela Oliveira Pisco" roles: @@ -395,7 +395,7 @@ build_info: output: "target/nextflow/workflows/ingestion/make_reference" executable: "target/nextflow/workflows/ingestion/make_reference/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/reference/make_reference" @@ -405,7 +405,7 @@ build_info: - "target/nextflow/reference/build_cellranger_arc_reference" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -435,7 +435,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/ingestion/make_reference/main.nf b/target/nextflow/workflows/ingestion/make_reference/main.nf index 0881b157..5aa61948 100644 --- a/target/nextflow/workflows/ingestion/make_reference/main.nf +++ b/target/nextflow/workflows/ingestion/make_reference/main.nf @@ -1,4 +1,4 @@ -// make_reference v4.0.1 +// make_reference v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "make_reference", "namespace" : "workflows/ingestion", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Angela Oliveira Pisco", @@ -3537,12 +3537,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/make_reference", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3567,7 +3567,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/ingestion/make_reference/nextflow.config b/target/nextflow/workflows/ingestion/make_reference/nextflow.config index 2ef0e8f5..378ca799 100644 --- a/target/nextflow/workflows/ingestion/make_reference/nextflow.config +++ b/target/nextflow/workflows/ingestion/make_reference/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/ingestion/make_reference' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Build a transcriptomics reference into one of many formats.\n' author = 'Angela Oliveira Pisco, Robrecht Cannoodt, Weiwei Schultz' } diff --git a/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml index ea054550..c125814f 100644 --- a/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/bbknn_leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bbknn_leiden" namespace: "workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Mauro Saporita" roles: @@ -335,7 +335,7 @@ build_info: output: "target/nextflow/workflows/integration/bbknn_leiden" executable: "target/nextflow/workflows/integration/bbknn_leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/cluster/leiden" @@ -344,7 +344,7 @@ build_info: - "target/nextflow/metadata/move_obsm_to_obs" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -374,7 +374,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/integration/bbknn_leiden/main.nf b/target/nextflow/workflows/integration/bbknn_leiden/main.nf index 2484c5a6..76dfdc1a 100644 --- a/target/nextflow/workflows/integration/bbknn_leiden/main.nf +++ b/target/nextflow/workflows/integration/bbknn_leiden/main.nf @@ -1,4 +1,4 @@ -// bbknn_leiden v4.0.1 +// bbknn_leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bbknn_leiden", "namespace" : "workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Mauro Saporita", @@ -3457,12 +3457,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/integration/bbknn_leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3487,7 +3487,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config b/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config index 65747c61..ed74b264 100644 --- a/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/bbknn_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/bbknn_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run bbknn followed by leiden clustering and run umap on the result.' author = 'Mauro Saporita, Povilas Gibas' } diff --git a/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml index 3d1c8484..236db522 100644 --- a/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/harmony_leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "harmony_leiden" namespace: "workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -363,7 +363,7 @@ build_info: output: "target/nextflow/workflows/integration/harmony_leiden" executable: "target/nextflow/workflows/integration/harmony_leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/integrate/harmonypy" @@ -373,7 +373,7 @@ build_info: - "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -403,7 +403,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/integration/harmony_leiden/main.nf b/target/nextflow/workflows/integration/harmony_leiden/main.nf index c00702ba..aabee603 100644 --- a/target/nextflow/workflows/integration/harmony_leiden/main.nf +++ b/target/nextflow/workflows/integration/harmony_leiden/main.nf @@ -1,4 +1,4 @@ -// harmony_leiden v4.0.1 +// harmony_leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "harmony_leiden", "namespace" : "workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3494,12 +3494,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/integration/harmony_leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3524,7 +3524,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/integration/harmony_leiden/nextflow.config b/target/nextflow/workflows/integration/harmony_leiden/nextflow.config index 01f71a81..992c0a80 100644 --- a/target/nextflow/workflows/integration/harmony_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/harmony_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/harmony_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run harmony integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml index 6d6be15c..97d16e1a 100644 --- a/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/scanorama_leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scanorama_leiden" namespace: "workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Mauro Saporita" roles: @@ -359,14 +359,14 @@ build_info: output: "target/nextflow/workflows/integration/scanorama_leiden" executable: "target/nextflow/workflows/integration/scanorama_leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/integrate/scanorama" - "target/nextflow/workflows/multiomics/neighbors_leiden_umap" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -396,7 +396,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/integration/scanorama_leiden/main.nf b/target/nextflow/workflows/integration/scanorama_leiden/main.nf index 530c1aa2..d6bacac6 100644 --- a/target/nextflow/workflows/integration/scanorama_leiden/main.nf +++ b/target/nextflow/workflows/integration/scanorama_leiden/main.nf @@ -1,4 +1,4 @@ -// scanorama_leiden v4.0.1 +// scanorama_leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scanorama_leiden", "namespace" : "workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Mauro Saporita", @@ -3489,12 +3489,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/integration/scanorama_leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3519,7 +3519,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config b/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config index e0e44aa4..1c3dc280 100644 --- a/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/scanorama_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/scanorama_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run scanorama integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Mauro Saporita, Povilas Gibas' } diff --git a/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml index c4d6c4bf..ad83855a 100644 --- a/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/scvi_leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "scvi_leiden" namespace: "workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -486,7 +486,7 @@ build_info: output: "target/nextflow/workflows/integration/scvi_leiden" executable: "target/nextflow/workflows/integration/scvi_leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/integrate/scvi" @@ -496,7 +496,7 @@ build_info: - "target/_private/nextflow/tiledb/move_mudata_obs_to_tiledb" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -526,7 +526,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/integration/scvi_leiden/main.nf b/target/nextflow/workflows/integration/scvi_leiden/main.nf index 8daaeb62..faa4c971 100644 --- a/target/nextflow/workflows/integration/scvi_leiden/main.nf +++ b/target/nextflow/workflows/integration/scvi_leiden/main.nf @@ -1,4 +1,4 @@ -// scvi_leiden v4.0.1 +// scvi_leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "scvi_leiden", "namespace" : "workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3618,12 +3618,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/integration/scvi_leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3648,7 +3648,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/integration/scvi_leiden/nextflow.config b/target/nextflow/workflows/integration/scvi_leiden/nextflow.config index 05657406..1cb091bf 100644 --- a/target/nextflow/workflows/integration/scvi_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/scvi_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/scvi_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run scvi integration followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml index ae8ebd84..7f56c22e 100644 --- a/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/totalvi_leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi_leiden" namespace: "workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dorien Roosen" roles: @@ -414,14 +414,14 @@ build_info: output: "target/nextflow/workflows/integration/totalvi_leiden" executable: "target/nextflow/workflows/integration/totalvi_leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/integrate/totalvi" - "target/nextflow/workflows/multiomics/neighbors_leiden_umap" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -451,7 +451,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/integration/totalvi_leiden/main.nf b/target/nextflow/workflows/integration/totalvi_leiden/main.nf index a7f9b6f9..eb1e459b 100644 --- a/target/nextflow/workflows/integration/totalvi_leiden/main.nf +++ b/target/nextflow/workflows/integration/totalvi_leiden/main.nf @@ -1,4 +1,4 @@ -// totalvi_leiden v4.0.1 +// totalvi_leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "totalvi_leiden", "namespace" : "workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dorien Roosen", @@ -3533,12 +3533,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/integration/totalvi_leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3563,7 +3563,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config b/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config index 91cc1151..9ae8d84c 100644 --- a/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/totalvi_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/totalvi_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run totalVI integration, followed by neighbour calculations, leiden clustering and UMAP.' author = 'Dorien Roosen' } diff --git a/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml b/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml index 05dfba5d..4ffcf513 100644 --- a/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/integration/totalvi_scarches_leiden/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "totalvi_scarches_leiden" namespace: "workflows/integration" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -496,14 +496,14 @@ build_info: output: "target/nextflow/workflows/integration/totalvi_scarches_leiden" executable: "target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/integrate/totalvi_scarches" - "target/nextflow/workflows/multiomics/neighbors_leiden_umap" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -533,7 +533,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf b/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf index de0f062d..c26581ff 100644 --- a/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf +++ b/target/nextflow/workflows/integration/totalvi_scarches_leiden/main.nf @@ -1,4 +1,4 @@ -// totalvi_scarches_leiden v4.0.1 +// totalvi_scarches_leiden v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "totalvi_scarches_leiden", "namespace" : "workflows/integration", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3634,12 +3634,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/integration/totalvi_scarches_leiden", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3664,7 +3664,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config b/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config index 723fb10f..c5dd7a85 100644 --- a/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config +++ b/target/nextflow/workflows/integration/totalvi_scarches_leiden/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/integration/totalvi_scarches_leiden' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run totalVI integration by mapping the query dataset to a reference, followed by neighbour calculations, leiden clustering and run umap on the result.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml b/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml index 7aa5cab7..42fb8216 100644 --- a/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "dimensionality_reduction" namespace: "workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -278,14 +278,14 @@ build_info: output: "target/nextflow/workflows/multiomics/dimensionality_reduction" executable: "target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/dimred/pca" - "target/nextflow/workflows/multiomics/neighbors_leiden_umap" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -315,7 +315,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf b/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf index 54b931ba..64de2ad2 100644 --- a/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf +++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf @@ -1,4 +1,4 @@ -// dimensionality_reduction v4.0.1 +// dimensionality_reduction v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "dimensionality_reduction", "namespace" : "workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3390,12 +3390,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/dimensionality_reduction", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3420,7 +3420,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config b/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config index ab1e05b1..1929ddf5 100644 --- a/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config +++ b/target/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/dimensionality_reduction' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Run calculations that output information required for most integration methods: PCA, nearest neighbour and UMAP.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml index 016f9f98..14ea936b 100644 --- a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "neighbors_leiden_umap" namespace: "workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -234,7 +234,7 @@ build_info: output: "target/nextflow/workflows/multiomics/neighbors_leiden_umap" executable: "target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/cluster/leiden" @@ -243,7 +243,7 @@ build_info: - "target/nextflow/metadata/move_obsm_to_obs" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -273,7 +273,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf index 7ef3f235..35b69c9f 100644 --- a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf +++ b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf @@ -1,4 +1,4 @@ -// neighbors_leiden_umap v4.0.1 +// neighbors_leiden_umap v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "neighbors_leiden_umap", "namespace" : "workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3331,12 +3331,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/neighbors_leiden_umap", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3361,7 +3361,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config index 470198fe..56a0a28f 100644 --- a/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config +++ b/target/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/neighbors_leiden_umap' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Performs neighborhood search, leiden clustering and run umap on an integrated embedding.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml b/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml index 0b6a5225..9108f093 100644 --- a/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "process_batches" namespace: "workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -380,7 +380,7 @@ build_info: output: "target/nextflow/workflows/multiomics/process_batches" executable: "target/nextflow/workflows/multiomics/process_batches/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/dataflow/merge" @@ -392,7 +392,7 @@ build_info: - "target/nextflow/workflows/multiomics/dimensionality_reduction" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -422,7 +422,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/multiomics/process_batches/main.nf b/target/nextflow/workflows/multiomics/process_batches/main.nf index ebcad2fb..fc200e36 100644 --- a/target/nextflow/workflows/multiomics/process_batches/main.nf +++ b/target/nextflow/workflows/multiomics/process_batches/main.nf @@ -1,4 +1,4 @@ -// process_batches v4.0.1 +// process_batches v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "process_batches", "namespace" : "workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3513,12 +3513,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/process_batches", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3543,7 +3543,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/multiomics/process_batches/nextflow.config b/target/nextflow/workflows/multiomics/process_batches/nextflow.config index f77ae890..8d44892e 100644 --- a/target/nextflow/workflows/multiomics/process_batches/nextflow.config +++ b/target/nextflow/workflows/multiomics/process_batches/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/process_batches' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'This workflow serves as an entrypoint into the \'full_pipeline\' in order to\nre-run the multisample processing and the integration setup. An input .h5mu file will \nfirst be split in order to run the multisample processing per modality. Next, the modalities\nare merged again and the integration setup pipeline is executed. Please note that this workflow\nassumes that samples from multiple pipelines are already concatenated. \n' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml index 8168b5d7..ab6c2eb8 100644 --- a/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "process_samples" namespace: "workflows/multiomics" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -711,7 +711,7 @@ build_info: output: "target/nextflow/workflows/multiomics/process_samples" executable: "target/nextflow/workflows/multiomics/process_samples/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/metadata/add_id" @@ -724,7 +724,7 @@ build_info: - "target/nextflow/workflows/multiomics/process_batches" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -754,7 +754,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/multiomics/process_samples/main.nf b/target/nextflow/workflows/multiomics/process_samples/main.nf index 068943c9..962f5608 100644 --- a/target/nextflow/workflows/multiomics/process_samples/main.nf +++ b/target/nextflow/workflows/multiomics/process_samples/main.nf @@ -1,4 +1,4 @@ -// process_samples v4.0.1 +// process_samples v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "process_samples", "namespace" : "workflows/multiomics", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3916,12 +3916,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/process_samples", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3946,7 +3946,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/multiomics/process_samples/nextflow.config b/target/nextflow/workflows/multiomics/process_samples/nextflow.config index e6c13878..e3c88deb 100644 --- a/target/nextflow/workflows/multiomics/process_samples/nextflow.config +++ b/target/nextflow/workflows/multiomics/process_samples/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/multiomics/process_samples' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A pipeline to analyse multiple multiomics samples.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml b/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml index 953d7cb1..088a5def 100644 --- a/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml +++ b/target/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "prot_multisample" namespace: "workflows/prot" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -284,14 +284,14 @@ build_info: output: "target/nextflow/workflows/prot/prot_multisample" executable: "target/nextflow/workflows/prot/prot_multisample/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/transform/clr" - "target/nextflow/workflows/qc/qc" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -321,7 +321,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/prot/prot_multisample/main.nf b/target/nextflow/workflows/prot/prot_multisample/main.nf index 99617f7e..4e5988f7 100644 --- a/target/nextflow/workflows/prot/prot_multisample/main.nf +++ b/target/nextflow/workflows/prot/prot_multisample/main.nf @@ -1,4 +1,4 @@ -// prot_multisample v4.0.1 +// prot_multisample v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "prot_multisample", "namespace" : "workflows/prot", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3384,12 +3384,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prot/prot_multisample", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3414,7 +3414,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/prot/prot_multisample/nextflow.config b/target/nextflow/workflows/prot/prot_multisample/nextflow.config index b284929b..f8e9137a 100644 --- a/target/nextflow/workflows/prot/prot_multisample/nextflow.config +++ b/target/nextflow/workflows/prot/prot_multisample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/prot/prot_multisample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Processing unimodal multi-sample ADT data.' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml b/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml index e30a6cc8..72504dd9 100644 --- a/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml +++ b/target/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "prot_singlesample" namespace: "workflows/prot" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -255,14 +255,14 @@ build_info: output: "target/nextflow/workflows/prot/prot_singlesample" executable: "target/nextflow/workflows/prot/prot_singlesample/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/filter/filter_with_counts" - "target/nextflow/filter/do_filter" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -292,7 +292,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/prot/prot_singlesample/main.nf b/target/nextflow/workflows/prot/prot_singlesample/main.nf index ebf1b7a4..dce38718 100644 --- a/target/nextflow/workflows/prot/prot_singlesample/main.nf +++ b/target/nextflow/workflows/prot/prot_singlesample/main.nf @@ -1,4 +1,4 @@ -// prot_singlesample v4.0.1 +// prot_singlesample v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "prot_singlesample", "namespace" : "workflows/prot", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3378,12 +3378,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prot/prot_singlesample", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3408,7 +3408,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/prot/prot_singlesample/nextflow.config b/target/nextflow/workflows/prot/prot_singlesample/nextflow.config index 48075db7..5935c8ba 100644 --- a/target/nextflow/workflows/prot/prot_singlesample/nextflow.config +++ b/target/nextflow/workflows/prot/prot_singlesample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/prot/prot_singlesample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Processing unimodal single-sample CITE-seq data.' author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont' } diff --git a/target/nextflow/workflows/qc/qc/.config.vsh.yaml b/target/nextflow/workflows/qc/qc/.config.vsh.yaml index c847e91c..8f825914 100644 --- a/target/nextflow/workflows/qc/qc/.config.vsh.yaml +++ b/target/nextflow/workflows/qc/qc/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "qc" namespace: "workflows/qc" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries Schaumont" roles: @@ -364,14 +364,14 @@ build_info: output: "target/nextflow/workflows/qc/qc" executable: "target/nextflow/workflows/qc/qc/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/metadata/grep_annotation_column" - "target/nextflow/qc/calculate_qc_metrics" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -401,7 +401,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/qc/qc/main.nf b/target/nextflow/workflows/qc/qc/main.nf index 158323c1..6b72517d 100644 --- a/target/nextflow/workflows/qc/qc/main.nf +++ b/target/nextflow/workflows/qc/qc/main.nf @@ -1,4 +1,4 @@ -// qc v4.0.1 +// qc v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "qc", "namespace" : "workflows/qc", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3471,12 +3471,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/qc/qc", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3501,7 +3501,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/qc/qc/nextflow.config b/target/nextflow/workflows/qc/qc/nextflow.config index 81668e63..c7c35650 100644 --- a/target/nextflow/workflows/qc/qc/nextflow.config +++ b/target/nextflow/workflows/qc/qc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/qc/qc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'A pipeline to add basic qc statistics to a MuData ' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml b/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml index 4c23e33a..62236dd0 100644 --- a/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml +++ b/target/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rna_multisample" namespace: "workflows/rna" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -422,7 +422,7 @@ build_info: output: "target/nextflow/workflows/rna/rna_multisample" executable: "target/nextflow/workflows/rna/rna_multisample/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/feature_annotation/highly_variable_features_scanpy" @@ -432,7 +432,7 @@ build_info: - "target/_private/nextflow/workflows/rna/log_normalize" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -462,7 +462,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/rna/rna_multisample/main.nf b/target/nextflow/workflows/rna/rna_multisample/main.nf index ac48dd2a..cfbe2256 100644 --- a/target/nextflow/workflows/rna/rna_multisample/main.nf +++ b/target/nextflow/workflows/rna/rna_multisample/main.nf @@ -1,4 +1,4 @@ -// rna_multisample v4.0.1 +// rna_multisample v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rna_multisample", "namespace" : "workflows/rna", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3557,12 +3557,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rna/rna_multisample", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3587,7 +3587,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/rna/rna_multisample/nextflow.config b/target/nextflow/workflows/rna/rna_multisample/nextflow.config index cc91db15..3656e522 100644 --- a/target/nextflow/workflows/rna/rna_multisample/nextflow.config +++ b/target/nextflow/workflows/rna/rna_multisample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/rna/rna_multisample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Processing unimodal multi-sample RNA transcriptomics data.' author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont' } diff --git a/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml b/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml index f89fd14b..f6bbb00f 100644 --- a/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml +++ b/target/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rna_singlesample" namespace: "workflows/rna" -version: "v4.0.1" +version: "v4.0.2" authors: - name: "Dries De Maeyer" roles: @@ -396,7 +396,7 @@ build_info: output: "target/nextflow/workflows/rna/rna_singlesample" executable: "target/nextflow/workflows/rna/rna_singlesample/main.nf" viash_version: "0.9.4" - git_commit: "e943ae3d1512ded126303c9481cb554d0dd38c92" + git_commit: "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62" git_remote: "https://github.com/openpipelines-bio/openpipeline" dependencies: - "target/nextflow/filter/filter_with_counts" @@ -406,7 +406,7 @@ build_info: - "target/nextflow/workflows/qc/qc" package_config: name: "openpipeline" - version: "v4.0.1" + version: "v4.0.2" summary: "Best-practice workflows for single-cell multi-omics analyses.\n" description: "OpenPipelines are extensible single cell analysis pipelines for reproducible\ \ and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\ @@ -436,7 +436,7 @@ package_config: )'" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + - ".engines[.type == 'docker'].target_tag := 'v4.0.2'" keywords: - "single-cell" - "multimodal" diff --git a/target/nextflow/workflows/rna/rna_singlesample/main.nf b/target/nextflow/workflows/rna/rna_singlesample/main.nf index 282159f3..11770dfb 100644 --- a/target/nextflow/workflows/rna/rna_singlesample/main.nf +++ b/target/nextflow/workflows/rna/rna_singlesample/main.nf @@ -1,4 +1,4 @@ -// rna_singlesample v4.0.1 +// rna_singlesample v4.0.2 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3037,7 +3037,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rna_singlesample", "namespace" : "workflows/rna", - "version" : "v4.0.1", + "version" : "v4.0.2", "authors" : [ { "name" : "Dries De Maeyer", @@ -3541,12 +3541,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rna/rna_singlesample", "viash_version" : "0.9.4", - "git_commit" : "e943ae3d1512ded126303c9481cb554d0dd38c92", + "git_commit" : "cd7beddfa85b60b543399a9e2554b8e7b8eaaf62", "git_remote" : "https://github.com/openpipelines-bio/openpipeline" }, "package_config" : { "name" : "openpipeline", - "version" : "v4.0.1", + "version" : "v4.0.2", "summary" : "Best-practice workflows for single-cell multi-omics analyses.\n", "description" : "OpenPipelines are extensible single cell analysis pipelines for reproducible and large-scale single cell processing using [Viash](https://viash.io) and [Nextflow](https://www.nextflow.io/).\n\nIn terms of workflows, the following has been made available, but keep in mind that\nindividual tools and functionality can be executed as standalone components as well.\n\n * Demultiplexing: conversion of raw sequencing data to FASTQ objects.\n * Ingestion: Read mapping and generating a count matrix.\n * Single sample processing: cell filtering and doublet detection.\n * Multisample processing: Count transformation, normalization, QC metric calulations.\n * Integration: Clustering, integration and batch correction using single and multimodal methods.\n * Downstream analysis workflows\n", "info" : { @@ -3571,7 +3571,7 @@ meta = [ ".resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v4.0.1'" + ".engines[.type == 'docker'].target_tag := 'v4.0.2'" ], "keywords" : [ "single-cell", diff --git a/target/nextflow/workflows/rna/rna_singlesample/nextflow.config b/target/nextflow/workflows/rna/rna_singlesample/nextflow.config index ed45fb90..42a2b9b7 100644 --- a/target/nextflow/workflows/rna/rna_singlesample/nextflow.config +++ b/target/nextflow/workflows/rna/rna_singlesample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/rna/rna_singlesample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v4.0.1' + version = 'v4.0.2' description = 'Processing unimodal single-sample RNA transcriptomics data.' author = 'Dries De Maeyer, Robrecht Cannoodt, Dries Schaumont' }