diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e3f24d..615834e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ * Bump squidpy to 1.8.1 and spatialdata to 0.7.2 (PR #41). -* Update openpipeline dependencies to v4.0.1 (PR #42). +* Update openpipeline dependencies to v4.0.2 (PR #42). # openpipeline_spatial 0.2.0 diff --git a/_viash.yaml b/_viash.yaml index 22cb387..7db3b34 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -10,7 +10,7 @@ repositories: - name: openpipeline repo: openpipeline type: vsh - tag: v4.0.1 + tag: v4.0.2 info: test_resources: - type: s3 diff --git a/src/workflows/niche/nichecompass_leiden/main.nf b/src/workflows/niche/nichecompass_leiden/main.nf index fb61449..440770a 100644 --- a/src/workflows/niche/nichecompass_leiden/main.nf +++ b/src/workflows/niche/nichecompass_leiden/main.nf @@ -28,7 +28,12 @@ workflow run_wf { | flatMap {id, state -> def outputDir = state.output - def files = readCsv(state.output_files.toUriString()) + + def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")} + def header = csv.head() + def files = csv.tail().collect { row -> + [header, row].transpose().collectEntries() + } files.collect{ dat -> def new_id = dat.name // unique sample ids diff --git a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml index a08492b..ee028f8 100644 --- a/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml +++ b/target/_private/executable/filter/subset_cosmx/.config.vsh.yaml @@ -112,7 +112,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -227,7 +227,7 @@ build_info: output: "target/_private/executable/filter/subset_cosmx" executable: "target/_private/executable/filter/subset_cosmx/subset_cosmx" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -241,7 +241,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/_private/executable/filter/subset_cosmx/subset_cosmx b/target/_private/executable/filter/subset_cosmx/subset_cosmx index 91b8f17..3bd3d9e 100755 --- a/target/_private/executable/filter/subset_cosmx/subset_cosmx +++ b/target/_private/executable/filter/subset_cosmx/subset_cosmx @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component filter subset_cosmx" -LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml index ac37fb5..0df52c4 100644 --- a/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml +++ b/target/_private/nextflow/filter/subset_cosmx/.config.vsh.yaml @@ -112,7 +112,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -227,7 +227,7 @@ build_info: output: "target/_private/nextflow/filter/subset_cosmx" executable: "target/_private/nextflow/filter/subset_cosmx/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -241,7 +241,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/_private/nextflow/filter/subset_cosmx/main.nf b/target/_private/nextflow/filter/subset_cosmx/main.nf index cd44a3a..41b0751 100644 --- a/target/_private/nextflow/filter/subset_cosmx/main.nf +++ b/target/_private/nextflow/filter/subset_cosmx/main.nf @@ -3187,7 +3187,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3333,7 +3333,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_private/nextflow/filter/subset_cosmx", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3353,7 +3353,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml b/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml index 5eb0d60..4681dcb 100644 --- a/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml @@ -48,7 +48,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -157,7 +157,7 @@ build_info: output: "target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test" executable: "target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -171,7 +171,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test b/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test index 04db757..4b8f409 100755 --- a/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test +++ b/target/_test/executable/test_workflows/ingestion/spaceranger_mapping_test/spaceranger_mapping_test @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/ingestion spaceranger_mapping_test" -LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml index 4fd87b1..64b62f2 100644 --- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml +++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml @@ -47,7 +47,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -156,7 +156,7 @@ build_info: output: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test" executable: "target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -170,7 +170,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test index 67fa3ce..3614bd6 100755 --- a/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test +++ b/target/_test/executable/test_workflows/niche/nichecompass_leiden_test/nichecompass_leiden_test @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component test_workflows/niche nichecompass_leiden_test" -LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml index 31a3adf..22efacb 100644 --- a/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/.config.vsh.yaml @@ -48,7 +48,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -157,7 +157,7 @@ build_info: output: "target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test" executable: "target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -171,7 +171,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf b/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf index 3eb0513..7164207 100644 --- a/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf +++ b/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test/main.nf @@ -3104,7 +3104,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3235,7 +3235,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/ingestion/spaceranger_mapping_test", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3255,7 +3255,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml index 5685230..0e8dcde 100644 --- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml +++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/.config.vsh.yaml @@ -47,7 +47,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -156,7 +156,7 @@ build_info: output: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test" executable: "target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -170,7 +170,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf index 4219af8..5c0cd06 100644 --- a/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf +++ b/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test/main.nf @@ -3104,7 +3104,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3235,7 +3235,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/_test/nextflow/test_workflows/niche/nichecompass_leiden_test", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3255,7 +3255,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml index 343a3c0..3d4b2af 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_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/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/main.nf index 01abda2..e1ba422 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_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/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config index 24eb55e..14e373d 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_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/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/multiomics/split_modalities/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/multiomics/split_modalities/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml index 2c4d359..e0c2fda 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_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/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/main.nf index b235513..d2e13de 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_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/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/nextflow.config index b8d823c..d3ea299 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_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/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/_private/nextflow/workflows/rna/log_normalize/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/_private/nextflow/workflows/rna/log_normalize/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/.config.vsh.yaml index 68a1032..e9d7e49 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/main.nf index ba1c8c6..6a5f549 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow.config index 83a52fd..bb4c68d 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/cluster/leiden/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/cluster/leiden/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml index 99df40d..05228f2 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/main.nf index f32e613..c12b5cd 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow.config index b8b3566..c716b1f 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/.config.vsh.yaml index 200bb1b..0cfdabb 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/main.nf index 9865569..fe4ec0a 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow.config index c57d078..f4d9aec 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/merge/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/merge/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/.config.vsh.yaml index 55e6f3f..c4c2d0a 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/main.nf index c31ca57..8737269 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow.config index d60d18b..0673119 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/.config.vsh.yaml index 55701c3..7b551c7 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/main.nf index ebda958..0fb4023 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow.config index 11770fe..49fb3fb 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_modalities/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_modalities/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/.config.vsh.yaml index 99356f0..da49ee6 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/main.nf index 74ddbcc..673a497 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow.config index 87744c8..4018099 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/pca/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/pca/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/.config.vsh.yaml index 7bf49da..fb378b9 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/main.nf index fc795e6..02a6940 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow.config index 67b7637..bc69bab 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dimred/umap/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dimred/umap/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml index 0049ddb..6985259 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf index 53c6419..e196e46 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config index d569616..7195163 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/subset_vars.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/subset_vars.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/feature_annotation/highly_variable_features_scanpy/subset_vars.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/feature_annotation/highly_variable_features_scanpy/subset_vars.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/.config.vsh.yaml index 1b073fa..1f2d5f9 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/main.nf index 3ce02f8..cd48505 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow.config index 973dd92..940bbae 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/delimit_fraction/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/delimit_fraction/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/.config.vsh.yaml index bf2bf73..c87bbf7 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/main.nf index 2f4a45f..6edcbde 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow.config index cea4cbb..461bcba 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/do_filter/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/do_filter/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/.config.vsh.yaml index 9b46a06..50aed5a 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/main.nf index b4d1a98..46b2812 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/nextflow.config index 648e1c8..1845720 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_counts/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_counts/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/.config.vsh.yaml index 72e1a60..3b33f09 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/main.nf index ad55056..cf79f99 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/nextflow.config index dab1008..533aa1c 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/filter/filter_with_scrublet/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/filter/filter_with_scrublet/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/.config.vsh.yaml index 64ad020..19b5bf3 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/main.nf index f994ca2..7b086f0 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/nextflow.config index 856076a..3360141 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/add_id/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/add_id/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/.config.vsh.yaml index dc167c4..3f828b2 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/main.nf index c069209..c22fa53 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/nextflow.config index 1d30120..08372d4 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/grep_annotation_column/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/grep_annotation_column/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml index 9a30337..0981699 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/main.nf index c7d9e0b..fa0b5ae 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/nextflow.config index 8d639c2..99670d0 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/metadata/move_obsm_to_obs/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/metadata/move_obsm_to_obs/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/.config.vsh.yaml index 155b39c..f8e4048 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/main.nf index 4f4d0bf..ea56e8e 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/nextflow.config index 4cf6f55..e164931 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/neighbors/find_neighbors/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/neighbors/find_neighbors/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml index 00fd9e5..c889842 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/main.nf index b532a6d..16a8261 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/nextflow.config index 3f5d4e0..ab6a39a 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/qc/calculate_qc_metrics/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/qc/calculate_qc_metrics/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/.config.vsh.yaml index 373d751..f3bc6d1 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/main.nf index 58b7f6b..eff671d 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/nextflow.config index 0ba7413..09cf62f 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/clr/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/clr/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/.config.vsh.yaml similarity index 97% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/.config.vsh.yaml index 3f4ef18..784cb41 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/main.nf index cce0333..9014366 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/nextflow.config index b935d69..1506cac 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/delete_layer/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/delete_layer/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/.config.vsh.yaml index 7bedc49..2684fe8 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/main.nf index bb74f56..78f335b 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/nextflow.config index 3362088..acc78f6 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/log1p/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/log1p/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/.config.vsh.yaml index 61aa3c9..6d7e887 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/main.nf index 2c519bb..c1d9e98 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/nextflow.config index b13f6a5..cd3f7e8 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/normalize_total/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/normalize_total/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/.config.vsh.yaml index 72fcb89..277f9c1 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/compress_h5mu.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/compress_h5mu.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/compress_h5mu.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/compress_h5mu.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/main.nf index 50a741c..4c62e9e 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/nextflow.config index b011135..8c0caa7 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/setup_logger.py b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/setup_logger.py similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/transform/scale/setup_logger.py rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/transform/scale/setup_logger.py diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml index 23fb8d4..be29f88 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/main.nf index 6b1a40d..f8b4b24 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/nextflow.config index 748fcab..5979bd8 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/gdo/gdo_singlesample/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/gdo/gdo_singlesample/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml index 7aa5cab..42fb821 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/main.nf index 54b931b..64de2ad 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config index ab1e05b..1929ddf 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/dimensionality_reduction/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml index 016f9f9..14ea936 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf index 7ef3f23..35b69c9 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config index 470198f..56a0a28 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml index 0b6a522..9108f09 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/main.nf index ebcad2f..fc200e3 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/nextflow.config index f77ae89..8d44892 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_batches/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_batches/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml index 8168b5d..ab6c2eb 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/main.nf index 068943c..962f560 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/nextflow.config index e6c1387..e3c88de 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml index 953d7cb..088a5de 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/main.nf index 99617f7..4e5988f 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/nextflow.config index b284929..f8e9137 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_multisample/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_multisample/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml index e30a6cc..72504dd 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/main.nf index ebf1b7a..dce3871 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/nextflow.config index 48075db..5935c8b 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/prot/prot_singlesample/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/prot/prot_singlesample/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/.config.vsh.yaml index c847e91..8f82591 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/main.nf index 158323c..6b72517 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/nextflow.config index 81668e6..c7c3565 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml index 4c23e33..62236dd 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/main.nf index ac48dd2..cfbe225 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/nextflow.config index cc91db1..3656e52 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_multisample/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_multisample/utils/labels_ci.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml similarity index 98% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml index f89fd14..f6bbb00 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/.config.vsh.yaml +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/main.nf b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/main.nf similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/main.nf rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/main.nf index 282159f..11770df 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/main.nf +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/nextflow.config similarity index 99% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/nextflow.config index ed45fb9..42a2b9b 100644 --- a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow.config +++ b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/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' } diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow_labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/nextflow_labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow_labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/nextflow_labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow_schema.json b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/nextflow_schema.json similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/nextflow_schema.json rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/nextflow_schema.json diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/errorstrat_ignore.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/errorstrat_ignore.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/errorstrat_ignore.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/errorstrat_ignore.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/integration_tests.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/integration_tests.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/integration_tests.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/integration_tests.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/labels.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/labels.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/labels.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/labels.config diff --git a/target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/labels_ci.config b/target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/labels_ci.config similarity index 100% rename from target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/rna/rna_singlesample/utils/labels_ci.config rename to target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/rna/rna_singlesample/utils/labels_ci.config diff --git a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index 4af9deb..e189982 100644 --- a/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cells2stats_to_h5mu/.config.vsh.yaml @@ -179,7 +179,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -303,7 +303,7 @@ build_info: output: "target/executable/convert/from_cells2stats_to_h5mu" executable: "target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -317,7 +317,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu index 1a3bfc9..e0f0ef5 100755 --- a/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu +++ b/target/executable/convert/from_cells2stats_to_h5mu/from_cells2stats_to_h5mu @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_cells2stats_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml index 59cabba..fef5c4f 100644 --- a/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -107,7 +107,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -239,7 +239,7 @@ build_info: output: "target/executable/convert/from_cosmx_to_h5mu" executable: "target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -253,7 +253,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu index 6b19c4d..981abf3 100755 --- a/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu +++ b/target/executable/convert/from_cosmx_to_h5mu/from_cosmx_to_h5mu @@ -460,9 +460,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-16T10:14:20Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index e0aa85c..bbda45f 100644 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -125,7 +125,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -234,7 +234,7 @@ build_info: output: "target/executable/convert/from_cosmx_to_spatialexperiment" executable: "target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -248,7 +248,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment index f7b03f3..9679c86 100755 --- a/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment +++ b/target/executable/convert/from_cosmx_to_spatialexperiment/from_cosmx_to_spatialexperiment @@ -457,9 +457,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_cosmx_to_spatialexperiment" -LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml index be0b62f..269fa42 100644 --- a/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml @@ -92,7 +92,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -227,7 +227,7 @@ build_info: output: "target/executable/convert/from_h5mu_to_spatialexperiment" executable: "target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -241,7 +241,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment index 4698ee9..c242323 100755 --- a/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment +++ b/target/executable/convert/from_h5mu_to_spatialexperiment/from_h5mu_to_spatialexperiment @@ -458,9 +458,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_h5mu_to_spatialexperiment" -LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_spaceranger_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_spaceranger_to_h5mu/.config.vsh.yaml index c440eef..607b2fa 100644 --- a/target/executable/convert/from_spaceranger_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_spaceranger_to_h5mu/.config.vsh.yaml @@ -144,7 +144,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -265,7 +265,7 @@ build_info: output: "target/executable/convert/from_spaceranger_to_h5mu" executable: "target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_to_h5mu" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -279,7 +279,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_to_h5mu b/target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_to_h5mu index 16b1eeb..de5edab 100755 --- a/target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_to_h5mu +++ b/target/executable/convert/from_spaceranger_to_h5mu/from_spaceranger_to_h5mu @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_spaceranger_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index dca3d2b..e0bfce4 100644 --- a/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -101,7 +101,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -223,7 +223,7 @@ build_info: output: "target/executable/convert/from_spatialdata_to_h5mu" executable: "target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -237,7 +237,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu index 0a345d5..4a762fe 100755 --- a/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu +++ b/target/executable/convert/from_spatialdata_to_h5mu/from_spatialdata_to_h5mu @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_spatialdata_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml index 3dc9c6e..9957a09 100644 --- a/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_h5mu/.config.vsh.yaml @@ -121,7 +121,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -246,7 +246,7 @@ build_info: output: "target/executable/convert/from_xenium_to_h5mu" executable: "target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -260,7 +260,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu index 388631e..48f1b7d 100755 --- a/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu +++ b/target/executable/convert/from_xenium_to_h5mu/from_xenium_to_h5mu @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_h5mu" -LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml index d886442..783e228 100644 --- a/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -201,7 +201,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -326,7 +326,7 @@ build_info: output: "target/executable/convert/from_xenium_to_spatialdata" executable: "target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -340,7 +340,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata index ad68949..c9e7e05 100755 --- a/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata +++ b/target/executable/convert/from_xenium_to_spatialdata/from_xenium_to_spatialdata @@ -459,9 +459,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen, Weiwei Schultz" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialdata" -LABEL org.opencontainers.image.created="2026-02-16T10:14:20Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:07Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 9eff008..8002095 100644 --- a/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/executable/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -115,7 +115,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -238,7 +238,7 @@ build_info: output: "target/executable/convert/from_xenium_to_spatialexperiment" executable: "target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -252,7 +252,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment index c059201..62c85b9 100755 --- a/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment +++ b/target/executable/convert/from_xenium_to_spatialexperiment/from_xenium_to_spatialexperiment @@ -462,9 +462,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component convert from_xenium_to_spatialexperiment" -LABEL org.opencontainers.image.created="2026-02-16T10:14:21Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/mapping/spaceranger_count/.config.vsh.yaml b/target/executable/mapping/spaceranger_count/.config.vsh.yaml index 8ad357d..9a24e03 100644 --- a/target/executable/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/executable/mapping/spaceranger_count/.config.vsh.yaml @@ -330,7 +330,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" keywords: - "spaceranger" links: @@ -439,7 +439,7 @@ build_info: output: "target/executable/mapping/spaceranger_count" executable: "target/executable/mapping/spaceranger_count/spaceranger_count" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -453,7 +453,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/mapping/spaceranger_count/spaceranger_count b/target/executable/mapping/spaceranger_count/spaceranger_count index 5ecd991..0d4b22f 100755 --- a/target/executable/mapping/spaceranger_count/spaceranger_count +++ b/target/executable/mapping/spaceranger_count/spaceranger_count @@ -453,9 +453,9 @@ apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.authors="Jakub Majercik" LABEL org.opencontainers.image.description="Companion container for running component mapping spaceranger_count" -LABEL org.opencontainers.image.created="2026-02-16T10:14:20Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:06Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml b/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml index 71fe63f..af35b5e 100644 --- a/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml +++ b/target/executable/neighbors/spatial_neighborhood_graph/.config.vsh.yaml @@ -147,7 +147,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -270,7 +270,7 @@ build_info: output: "target/executable/neighbors/spatial_neighborhood_graph" executable: "target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -284,7 +284,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph b/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph index 0c65426..c02c371 100755 --- a/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph +++ b/target/executable/neighbors/spatial_neighborhood_graph/spatial_neighborhood_graph @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component neighbors spatial_neighborhood_graph" -LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/executable/nichecompass/nichecompass/.config.vsh.yaml b/target/executable/nichecompass/nichecompass/.config.vsh.yaml index aa8b37c..b3fc611 100644 --- a/target/executable/nichecompass/nichecompass/.config.vsh.yaml +++ b/target/executable/nichecompass/nichecompass/.config.vsh.yaml @@ -875,7 +875,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -998,7 +998,7 @@ build_info: output: "target/executable/nichecompass/nichecompass" executable: "target/executable/nichecompass/nichecompass/nichecompass" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -1012,7 +1012,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/executable/nichecompass/nichecompass/nichecompass b/target/executable/nichecompass/nichecompass/nichecompass index 28e75f8..0caaac1 100755 --- a/target/executable/nichecompass/nichecompass/nichecompass +++ b/target/executable/nichecompass/nichecompass/nichecompass @@ -460,9 +460,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dorien Roosen" LABEL org.opencontainers.image.description="Companion container for running component nichecompass nichecompass" -LABEL org.opencontainers.image.created="2026-02-16T10:14:22Z" +LABEL org.opencontainers.image.created="2026-02-16T13:09:08Z" LABEL org.opencontainers.image.source="https://github.com/openpipelines-bio/openpipeline_spatial" -LABEL org.opencontainers.image.revision="1d17a50229be6fb6702bda689aada82de1c9c56c" +LABEL org.opencontainers.image.revision="86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" LABEL org.opencontainers.image.version="niche-compass" VIASHDOCKER diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml index d8d6d46..1f44ee8 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cells2stats_to_h5mu/.config.vsh.yaml @@ -179,7 +179,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -303,7 +303,7 @@ build_info: output: "target/nextflow/convert/from_cells2stats_to_h5mu" executable: "target/nextflow/convert/from_cells2stats_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -317,7 +317,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf index 613522e..80475fd 100644 --- a/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cells2stats_to_h5mu/main.nf @@ -3246,7 +3246,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3400,7 +3400,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cells2stats_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3420,7 +3420,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml index 13e5b4e..8f34df3 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_h5mu/.config.vsh.yaml @@ -107,7 +107,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -239,7 +239,7 @@ build_info: output: "target/nextflow/convert/from_cosmx_to_h5mu" executable: "target/nextflow/convert/from_cosmx_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -253,7 +253,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf index 24702c6..05a4ac9 100644 --- a/target/nextflow/convert/from_cosmx_to_h5mu/main.nf +++ b/target/nextflow/convert/from_cosmx_to_h5mu/main.nf @@ -3184,7 +3184,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3350,7 +3350,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3370,7 +3370,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml index 7a55348..658d5ce 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/.config.vsh.yaml @@ -125,7 +125,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -234,7 +234,7 @@ build_info: output: "target/nextflow/convert/from_cosmx_to_spatialexperiment" executable: "target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -248,7 +248,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf index bb2f2ec..477c20b 100644 --- a/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_cosmx_to_spatialexperiment/main.nf @@ -3190,7 +3190,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3326,7 +3326,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_cosmx_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3346,7 +3346,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml index 8716d64..116178d 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/.config.vsh.yaml @@ -92,7 +92,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -227,7 +227,7 @@ build_info: output: "target/nextflow/convert/from_h5mu_to_spatialexperiment" executable: "target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -241,7 +241,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf index 3b3b698..ba4c1f2 100644 --- a/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_h5mu_to_spatialexperiment/main.nf @@ -3163,7 +3163,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3334,7 +3334,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_h5mu_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3354,7 +3354,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_spaceranger_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_spaceranger_to_h5mu/.config.vsh.yaml index 331cbf6..a8dba59 100644 --- a/target/nextflow/convert/from_spaceranger_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_spaceranger_to_h5mu/.config.vsh.yaml @@ -144,7 +144,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -265,7 +265,7 @@ build_info: output: "target/nextflow/convert/from_spaceranger_to_h5mu" executable: "target/nextflow/convert/from_spaceranger_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -279,7 +279,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_spaceranger_to_h5mu/main.nf b/target/nextflow/convert/from_spaceranger_to_h5mu/main.nf index de1a0a0..9798479 100644 --- a/target/nextflow/convert/from_spaceranger_to_h5mu/main.nf +++ b/target/nextflow/convert/from_spaceranger_to_h5mu/main.nf @@ -3217,7 +3217,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3368,7 +3368,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_spaceranger_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3388,7 +3388,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml index 173d070..a8bf50b 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/.config.vsh.yaml @@ -101,7 +101,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -223,7 +223,7 @@ build_info: output: "target/nextflow/convert/from_spatialdata_to_h5mu" executable: "target/nextflow/convert/from_spatialdata_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -237,7 +237,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf index 12f8351..f3d2310 100644 --- a/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf +++ b/target/nextflow/convert/from_spatialdata_to_h5mu/main.nf @@ -3180,7 +3180,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3332,7 +3332,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_spatialdata_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3352,7 +3352,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml index 5350895..5134dd2 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_h5mu/.config.vsh.yaml @@ -121,7 +121,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -246,7 +246,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_h5mu" executable: "target/nextflow/convert/from_xenium_to_h5mu/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -260,7 +260,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_xenium_to_h5mu/main.nf b/target/nextflow/convert/from_xenium_to_h5mu/main.nf index 005ccaf..58be9ea 100644 --- a/target/nextflow/convert/from_xenium_to_h5mu/main.nf +++ b/target/nextflow/convert/from_xenium_to_h5mu/main.nf @@ -3194,7 +3194,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3349,7 +3349,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_h5mu", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3369,7 +3369,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml index fcc872f..865c629 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialdata/.config.vsh.yaml @@ -201,7 +201,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -326,7 +326,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_spatialdata" executable: "target/nextflow/convert/from_xenium_to_spatialdata/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -340,7 +340,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf index 672869d..09fb4e1 100644 --- a/target/nextflow/convert/from_xenium_to_spatialdata/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialdata/main.nf @@ -3283,7 +3283,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3443,7 +3443,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialdata", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3463,7 +3463,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml index 3d51d4f..06cfc81 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/.config.vsh.yaml @@ -115,7 +115,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -238,7 +238,7 @@ build_info: output: "target/nextflow/convert/from_xenium_to_spatialexperiment" executable: "target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -252,7 +252,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf index 3edc4d6..9e46b22 100644 --- a/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf +++ b/target/nextflow/convert/from_xenium_to_spatialexperiment/main.nf @@ -3179,7 +3179,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3337,7 +3337,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/convert/from_xenium_to_spatialexperiment", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3357,7 +3357,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml index 809f115..67b6ee0 100644 --- a/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml +++ b/target/nextflow/mapping/spaceranger_count/.config.vsh.yaml @@ -330,7 +330,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" keywords: - "spaceranger" links: @@ -439,7 +439,7 @@ build_info: output: "target/nextflow/mapping/spaceranger_count" executable: "target/nextflow/mapping/spaceranger_count/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -453,7 +453,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/mapping/spaceranger_count/main.nf b/target/nextflow/mapping/spaceranger_count/main.nf index d39227e..a2031cb 100644 --- a/target/nextflow/mapping/spaceranger_count/main.nf +++ b/target/nextflow/mapping/spaceranger_count/main.nf @@ -3433,7 +3433,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "keywords" : [ @@ -3569,7 +3569,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/mapping/spaceranger_count", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3589,7 +3589,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml b/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml index 3a5b2f2..0f4fb37 100644 --- a/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml +++ b/target/nextflow/neighbors/spatial_neighborhood_graph/.config.vsh.yaml @@ -147,7 +147,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -270,7 +270,7 @@ build_info: output: "target/nextflow/neighbors/spatial_neighborhood_graph" executable: "target/nextflow/neighbors/spatial_neighborhood_graph/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -284,7 +284,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf b/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf index bb0c7db..44c9cc2 100644 --- a/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf +++ b/target/nextflow/neighbors/spatial_neighborhood_graph/main.nf @@ -3220,7 +3220,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3373,7 +3373,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/neighbors/spatial_neighborhood_graph", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3393,7 +3393,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml b/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml index 516a7b1..895aa1e 100644 --- a/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml +++ b/target/nextflow/nichecompass/nichecompass/.config.vsh.yaml @@ -875,7 +875,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -998,7 +998,7 @@ build_info: output: "target/nextflow/nichecompass/nichecompass" executable: "target/nextflow/nichecompass/nichecompass/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" package_config: name: "openpipeline_spatial" @@ -1012,7 +1012,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/nichecompass/nichecompass/main.nf b/target/nextflow/nichecompass/nichecompass/main.nf index 405149b..24a718a 100644 --- a/target/nextflow/nichecompass/nichecompass/main.nf +++ b/target/nextflow/nichecompass/nichecompass/main.nf @@ -3979,7 +3979,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -4129,7 +4129,7 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/nichecompass/nichecompass", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -4149,7 +4149,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/workflows/ingestion/spaceranger_mapping/.config.vsh.yaml b/target/nextflow/workflows/ingestion/spaceranger_mapping/.config.vsh.yaml index 6778eb0..84d0330 100644 --- a/target/nextflow/workflows/ingestion/spaceranger_mapping/.config.vsh.yaml +++ b/target/nextflow/workflows/ingestion/spaceranger_mapping/.config.vsh.yaml @@ -399,7 +399,7 @@ repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -477,7 +477,7 @@ build_info: output: "target/nextflow/workflows/ingestion/spaceranger_mapping" executable: "target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - "target/nextflow/mapping/spaceranger_count" @@ -494,7 +494,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf b/target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf index d472581..b9aa42b 100644 --- a/target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf +++ b/target/nextflow/workflows/ingestion/spaceranger_mapping/main.nf @@ -3532,7 +3532,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3623,7 +3623,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/ingestion/spaceranger_mapping", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3643,7 +3643,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml index 7cc123c..957e3a1 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/.config.vsh.yaml @@ -557,12 +557,12 @@ dependencies: repository: type: "vsh" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -640,10 +640,10 @@ build_info: output: "target/nextflow/workflows/multiomics/spatial_process_samples" executable: "target/nextflow/workflows/multiomics/spatial_process_samples/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - - "target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples" + - "target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples" package_config: name: "openpipeline_spatial" version: "niche-compass" @@ -656,7 +656,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf index ce0db5e..3954aa6 100644 --- a/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf +++ b/target/nextflow/workflows/multiomics/spatial_process_samples/main.nf @@ -3707,7 +3707,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } } ], @@ -3716,7 +3716,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3807,7 +3807,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/multiomics/spatial_process_samples", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3827,7 +3827,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", @@ -3850,7 +3850,7 @@ meta = [ // resolve dependencies dependencies (if any) meta["root_dir"] = getRootDir() -include { process_samples as spatial_sample_processing_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/process_samples/main.nf" +include { process_samples as spatial_sample_processing_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/process_samples/main.nf" spatial_sample_processing = spatial_sample_processing_viashalias.run(key: "spatial_sample_processing") // inner workflow diff --git a/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml b/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml index ad11c9f..98884e2 100644 --- a/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml +++ b/target/nextflow/workflows/niche/nichecompass_leiden/.config.vsh.yaml @@ -698,7 +698,7 @@ dependencies: repository: type: "vsh" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" - name: "neighbors/spatial_neighborhood_graph" repository: type: "local" @@ -709,17 +709,17 @@ dependencies: repository: type: "vsh" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" - name: "workflows/multiomics/neighbors_leiden_umap" repository: type: "vsh" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -797,14 +797,14 @@ build_info: output: "target/nextflow/workflows/niche/nichecompass_leiden" executable: "target/nextflow/workflows/niche/nichecompass_leiden/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - - "target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu" + - "target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu" - "target/nextflow/neighbors/spatial_neighborhood_graph" - "target/nextflow/nichecompass/nichecompass" - - "target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu" - - "target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap" + - "target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu" + - "target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap" package_config: name: "openpipeline_spatial" version: "niche-compass" @@ -817,7 +817,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/workflows/niche/nichecompass_leiden/main.nf b/target/nextflow/workflows/niche/nichecompass_leiden/main.nf index b62693a..0516b9b 100644 --- a/target/nextflow/workflows/niche/nichecompass_leiden/main.nf +++ b/target/nextflow/workflows/niche/nichecompass_leiden/main.nf @@ -3822,7 +3822,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } }, { @@ -3842,7 +3842,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } }, { @@ -3850,7 +3850,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } } ], @@ -3859,7 +3859,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3950,7 +3950,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/niche/nichecompass_leiden", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3970,7 +3970,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", @@ -3993,11 +3993,11 @@ meta = [ // resolve dependencies dependencies (if any) meta["root_dir"] = getRootDir() -include { concatenate_h5mu } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/concatenate_h5mu/main.nf" +include { concatenate_h5mu } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/concatenate_h5mu/main.nf" include { spatial_neighborhood_graph } from "${meta.resources_dir}/../../../../nextflow/neighbors/spatial_neighborhood_graph/main.nf" include { nichecompass } from "${meta.resources_dir}/../../../../nextflow/nichecompass/nichecompass/main.nf" -include { split_h5mu } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/dataflow/split_h5mu/main.nf" -include { neighbors_leiden_umap } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf" +include { split_h5mu } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/dataflow/split_h5mu/main.nf" +include { neighbors_leiden_umap } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/multiomics/neighbors_leiden_umap/main.nf" // inner workflow // user-provided Nextflow code @@ -4031,7 +4031,12 @@ workflow run_wf { | flatMap {id, state -> def outputDir = state.output - def files = readCsv(state.output_files.toUriString()) + + def csv = state.output_files.splitCsv(strip: true, sep: ",").findAll{!it[0].startsWith("#")} + def header = csv.head() + def files = csv.tail().collect { row -> + [header, row].transpose().collectEntries() + } files.collect{ dat -> def new_id = dat.name // unique sample ids diff --git a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml index b6682b8..dd59aa4 100644 --- a/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml +++ b/target/nextflow/workflows/qc/spatial_qc/.config.vsh.yaml @@ -304,12 +304,12 @@ dependencies: repository: type: "vsh" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" repositories: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" links: repository: "https://github.com/openpipelines-bio/openpipeline_spatial" docker_registry: "ghcr.io" @@ -387,10 +387,10 @@ build_info: output: "target/nextflow/workflows/qc/spatial_qc" executable: "target/nextflow/workflows/qc/spatial_qc/main.nf" viash_version: "0.9.4" - git_commit: "1d17a50229be6fb6702bda689aada82de1c9c56c" + git_commit: "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc" git_remote: "https://github.com/openpipelines-bio/openpipeline_spatial" dependencies: - - "target/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc" + - "target/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc" package_config: name: "openpipeline_spatial" version: "niche-compass" @@ -403,7 +403,7 @@ package_config: - type: "vsh" name: "openpipeline" repo: "openpipeline" - tag: "v4.0.1" + tag: "v4.0.2" viash_version: "0.9.4" source: "src" target: "target" diff --git a/target/nextflow/workflows/qc/spatial_qc/main.nf b/target/nextflow/workflows/qc/spatial_qc/main.nf index a86a1dd..852abff 100644 --- a/target/nextflow/workflows/qc/spatial_qc/main.nf +++ b/target/nextflow/workflows/qc/spatial_qc/main.nf @@ -3405,7 +3405,7 @@ meta = [ "repository" : { "type" : "vsh", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } } ], @@ -3414,7 +3414,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "links" : { @@ -3505,7 +3505,7 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/qc/spatial_qc", "viash_version" : "0.9.4", - "git_commit" : "1d17a50229be6fb6702bda689aada82de1c9c56c", + "git_commit" : "86d15c1b0d1bdc77c2adffaa09f98f28045fa5bc", "git_remote" : "https://github.com/openpipelines-bio/openpipeline_spatial" }, "package_config" : { @@ -3525,7 +3525,7 @@ meta = [ "type" : "vsh", "name" : "openpipeline", "repo" : "openpipeline", - "tag" : "v4.0.1" + "tag" : "v4.0.2" } ], "viash_version" : "0.9.4", @@ -3548,7 +3548,7 @@ meta = [ // resolve dependencies dependencies (if any) meta["root_dir"] = getRootDir() -include { qc as spatial_qc_workflow_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.1/nextflow/workflows/qc/qc/main.nf" +include { qc as spatial_qc_workflow_viashalias } from "${meta.root_dir}/dependencies/vsh/vsh/openpipeline/v4.0.2/nextflow/workflows/qc/qc/main.nf" spatial_qc_workflow = spatial_qc_workflow_viashalias.run(key: "spatial_qc_workflow") // inner workflow