diff --git a/CHANGELOG.md b/CHANGELOG.md index e7c3292a..2f9e6225 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# htrnaseq v0.5.2 + +## Bug fixes + +* `create_fdata`: remove duplicate entries from feature data (PR #41). + # htrnaseq v0.5.1 ## Bug fixes diff --git a/_viash.yaml b/_viash.yaml index c422d183..0392f869 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.5.1 +version: v0.5.2 description: | High-throughput pipeline [WIP] license: MIT diff --git a/src/eset/create_fdata/create_fdata.py b/src/eset/create_fdata/create_fdata.py index 6b2a91b4..175007a4 100644 --- a/src/eset/create_fdata/create_fdata.py +++ b/src/eset/create_fdata/create_fdata.py @@ -119,10 +119,17 @@ def main(par): idx, cols = pd.factorize(column_to_get) symbol_values = annotation.reindex(cols, axis=1).to_numpy()[np.arange(len(annotation)), idx] annotation["SYMBOL"] = symbol_values - - logger.info("Writing to %s", par["output"]) + logger.info("Dropping unused columns") annotation = annotation.drop(["score", "source", "frame", "feature"], axis=1) + logger.info("Looking for duplicate rows and removing them. Starting with %i entries", annotation.shape[0]) + annotation = annotation.drop_duplicates(keep="first", ignore_index=True) + logger.info("After removing duplicates: %i entries", annotation.shape[0]) + logger.info("Writing to %s", par["output"]) annotation.to_csv(par["output"], sep="\t", header=True, index=False, na_rep="NA") + # Do these checks *after* writing the csv in order to be able to check the data + logger.info("Checking for unique gene IDs") + if not annotation["gene_id"].is_unique: + raise ValueError("Values from the 'gene_id' column are not unique after processing!") logger.info("%s finished", meta['name']) diff --git a/src/eset/create_fdata/test.py b/src/eset/create_fdata/test.py index 312d1353..b80ebfac 100644 --- a/src/eset/create_fdata/test.py +++ b/src/eset/create_fdata/test.py @@ -3,6 +3,7 @@ import sys import pandas as pd from pathlib import Path from uuid import uuid4 +from shutil import copyfile ### VIASH START meta = { @@ -57,5 +58,45 @@ def test_create_fdata(run_component, test_annotation_path, random_path): pd.testing.assert_frame_equal(expected, result, check_like=True) +def test_make_unique(run_component, test_annotation_path, random_path): + gtf_with_duplicate_entry_path = random_path("gtf") + output_path = random_path("tsv") + entry_to_add = ( + "\n20 ensembl_havana gene 87250 97094 . + . gene_id " + + "\"ENSG00000178591.7\"; gene_version \"7\"; gene_name \"DEFB125\"; " + + "gene_source \"ensembl_havana\"; gene_biotype \"protein_coding\";\n" + ) + copyfile(test_annotation_path, gtf_with_duplicate_entry_path) + with gtf_with_duplicate_entry_path.open("a") as open_gtf: + open_gtf.write(entry_to_add) + run_component([ + "--gtf", gtf_with_duplicate_entry_path, + "--output", output_path + ]) + assert output_path.is_file() + result = pd.read_csv(output_path, sep="\t", dtype=pd.StringDtype()) + expected_dict = { + "seqname": ["20", "20", "20", "21"], + "start": ["87250", "142590", "157454", "297570"], + "end": ["97094", "145751", "159163", "300321"], + "strand": ["+", "+", "+", "+"], + "gene_id": ["ENSG00000178591", "ENSG00000125788", + "ENSG00000088782", "ENSG00000247315"], + "gene_version": ["7", "6", "5", "4"], + "gene_name": ["DEFB125", "DEFB126", "DEFB127", pd.NA], + "gene_source": ["ensembl_havana", "ensembl_havana", + "ensembl_havana", "havana"], + "gene_biotype": ["protein_coding", "protein_coding", + "protein_coding", "protein_coding"], + "ENSEMBL_with_version": ["ENSG00000178591.7", "ENSG00000125788", + "ENSG00000088782", "ENSG00000247315"], + "ENSEMBL": ["ENSG00000178591", "ENSG00000125788", + "ENSG00000088782", "ENSG00000247315"], + "SYMBOL": ["DEFB125", "DEFB126", "DEFB127", pd.NA] + } + expected = pd.DataFrame.from_dict(expected_dict, dtype=pd.StringDtype()) + pd.testing.assert_frame_equal(expected, result, check_like=True) + + if __name__ == '__main__': sys.exit(pytest.main([__file__])) \ No newline at end of file diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 0c717a1d..8da138a4 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_eset" namespace: "eset" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -172,7 +172,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "r" @@ -198,11 +198,11 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +217,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index d34d9a17..f945d6c9 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_eset v0.5.1 +# create_eset v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_eset v0.5.1" + echo "create_eset v0.5.2" echo "" echo "Arguments:" echo " --pDataFile" @@ -477,10 +477,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_eset" -LABEL org.opencontainers.image.created="2025-02-17T07:53:55Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:27Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -616,7 +616,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_eset v0.5.1" + echo "create_eset v0.5.2" exit ;; --pDataFile) @@ -768,7 +768,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.5.2' fi # print dockerfile diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 065645ce..b1fc88fa 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_fdata" namespace: "eset" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -148,7 +148,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -177,11 +177,11 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -196,7 +196,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 0d576a12..12aca199 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_fdata v0.5.1 +# create_fdata v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_fdata v0.5.1" + echo "create_fdata v0.5.2" echo "" echo "Create a fdata file" echo "" @@ -478,10 +478,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-02-17T07:53:56Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:28Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -617,7 +617,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_fdata v0.5.1" + echo "create_fdata v0.5.2" exit ;; --gtf) @@ -730,7 +730,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.5.2' fi # print dockerfile @@ -1162,10 +1162,17 @@ def main(par): idx, cols = pd.factorize(column_to_get) symbol_values = annotation.reindex(cols, axis=1).to_numpy()[np.arange(len(annotation)), idx] annotation["SYMBOL"] = symbol_values - - logger.info("Writing to %s", par["output"]) + logger.info("Dropping unused columns") annotation = annotation.drop(["score", "source", "frame", "feature"], axis=1) + logger.info("Looking for duplicate rows and removing them. Starting with %i entries", annotation.shape[0]) + annotation = annotation.drop_duplicates(keep="first", ignore_index=True) + logger.info("After removing duplicates: %i entries", annotation.shape[0]) + logger.info("Writing to %s", par["output"]) annotation.to_csv(par["output"], sep="\\t", header=True, index=False, na_rep="NA") + # Do these checks *after* writing the csv in order to be able to check the data + logger.info("Checking for unique gene IDs") + if not annotation["gene_id"].is_unique: + raise ValueError("Values from the 'gene_id' column are not unique after processing!") logger.info("%s finished", meta['name']) diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 0617e278..f16b83bd 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pdata" namespace: "eset" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -191,11 +191,11 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -210,7 +210,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index cf9e7868..f172b45a 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_pdata v0.5.1 +# create_pdata v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pdata v0.5.1" + echo "create_pdata v0.5.2" echo "" echo "Create a pdata file by combining the mapping statistics" echo "" @@ -488,10 +488,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-02-17T07:53:55Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:27Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -627,7 +627,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pdata v0.5.1" + echo "create_pdata v0.5.2" exit ;; --star_stats_file) @@ -751,7 +751,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.5.2' fi # print dockerfile diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 81847d58..309c5b0a 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_eset" namespace: "integration_test_components/htrnaseq" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "r" @@ -148,11 +148,11 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -167,7 +167,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index 643c2718..c965502d 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# check_eset v0.5.1 +# check_eset v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_eset v0.5.1" + echo "check_eset v0.5.2" echo "" echo "This component test the ExpressionSet object as output by the main pipeline." echo "" @@ -470,10 +470,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset" -LABEL org.opencontainers.image.created="2025-02-17T07:53:55Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:27Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_eset v0.5.1" + echo "check_eset v0.5.2" exit ;; --eset) @@ -728,7 +728,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.5.2' fi # print dockerfile diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 13bd7b29..33a69c3c 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_cutadapt_output" namespace: "integration_test_components/well_demultiplexing" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -135,7 +135,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -158,11 +158,11 @@ build_info: output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -177,7 +177,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output index 065380c2..47686f76 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# check_cutadapt_output v0.5.1 +# check_cutadapt_output v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_cutadapt_output v0.5.1" + echo "check_cutadapt_output v0.5.2" echo "" echo "This component test the cutadapt output from the well_demultiplex subworkflow." echo "" @@ -476,10 +476,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-02-17T07:53:55Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:27Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_cutadapt_output v0.5.1" + echo "check_cutadapt_output v0.5.2" exit ;; --fastq_r1) @@ -757,7 +757,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.5.2' fi # print dockerfile diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index d2399a93..f9acbece 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_fastqs" namespace: "io" -version: "v0.5.1" +version: "v0.5.2" argument_groups: - name: "Input arguments" arguments: @@ -125,7 +125,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -143,11 +143,11 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -162,7 +162,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index ebfdcecc..8708b1b4 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish_fastqs v0.5.1 +# publish_fastqs v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_fastqs v0.5.1" + echo "publish_fastqs v0.5.2" echo "" echo "Publish the fastq files per well" echo "" @@ -470,10 +470,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-02-17T07:53:54Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:26Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_fastqs v0.5.1" + echo "publish_fastqs v0.5.2" exit ;; --input_r1) @@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.5.2' fi # print dockerfile diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index c5026d6c..a915ed0e 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_results" namespace: "io" -version: "v0.5.1" +version: "v0.5.2" argument_groups: - name: "Input arguments" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -187,11 +187,11 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -206,7 +206,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 8781ede3..68f308dc 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish_results v0.5.1 +# publish_results v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_results v0.5.1" + echo "publish_results v0.5.2" echo "" echo "Publish the results" echo "" @@ -484,10 +484,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-02-17T07:53:54Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:26Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -623,7 +623,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_results v0.5.1" + echo "publish_results v0.5.2" exit ;; --star_output) @@ -838,7 +838,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.5.2' fi # print dockerfile diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 64fe1814..2b1f62af 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "parallel_map" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -242,7 +242,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -298,7 +298,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index 3a16abb8..4d809eda 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# parallel_map v0.5.1 +# parallel_map v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "parallel_map v0.5.1" + echo "parallel_map v0.5.2" echo "" echo "Map wells in batch, using STAR" echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin" @@ -540,10 +540,10 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-02-17T07:53:56Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:28Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -679,7 +679,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "parallel_map v0.5.1" + echo "parallel_map v0.5.2" exit ;; --input_r1) @@ -881,7 +881,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.5.2' fi # print dockerfile diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 957164e5..13aaa1ff 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_report" namespace: "report" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -201,11 +201,11 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -220,7 +220,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 10cd1ec5..11ee057f 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_report v0.5.1 +# create_report v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_report v0.5.1" + echo "create_report v0.5.2" echo "" echo "Create a basic QC report in HTML format based on a number of esets." echo "" @@ -476,10 +476,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component report create_report" -LABEL org.opencontainers.image.created="2025-02-17T07:53:56Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:28Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_report v0.5.1" + echo "create_report v0.5.2" exit ;; --eset) @@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.5.2' fi # print dockerfile diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 324e4923..5cd1dfd7 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_star_logs" namespace: "stats" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -169,7 +169,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,11 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +217,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 1e498709..8982a7e4 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# combine_star_logs v0.5.1 +# combine_star_logs v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "combine_star_logs v0.5.1" + echo "combine_star_logs v0.5.2" echo "" echo "Arguments:" echo " --barcodes" @@ -490,10 +490,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-02-17T07:53:54Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:26Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "combine_star_logs v0.5.1" + echo "combine_star_logs v0.5.2" exit ;; --barcodes) @@ -799,7 +799,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.5.2' fi # print dockerfile diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index a7cfdaef..fb3ba3b5 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_pool_statistics" namespace: "stats" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -182,11 +182,11 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -201,7 +201,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 4bc5487a..ff881cd2 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# generate_pool_statistics v0.5.1 +# generate_pool_statistics v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_pool_statistics v0.5.1" + echo "generate_pool_statistics v0.5.2" echo "" echo "Arguments:" echo " --nrReadsNrGenesPerChrom" @@ -483,10 +483,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-02-17T07:53:54Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:26Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_pool_statistics v0.5.1" + echo "generate_pool_statistics v0.5.2" exit ;; --nrReadsNrGenesPerChrom) @@ -741,7 +741,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.5.2' fi # print dockerfile diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index 65b5f1f2..24b6166a 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_well_statistics" namespace: "stats" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,11 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -283,7 +283,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index a51ab7b6..e1898245 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# generate_well_statistics v0.5.1 +# generate_well_statistics v0.5.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_well_statistics v0.5.1" + echo "generate_well_statistics v0.5.2" echo "" echo "Generate summary statistics from BAM files generated by STAR solo." echo "" @@ -520,10 +520,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-02-17T07:53:55Z" +LABEL org.opencontainers.image.created="2025-02-17T15:02:27Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="73afe64a7776924434bdf6e66dee26f2f6c6246d" -LABEL org.opencontainers.image.version="v0.5.1" +LABEL org.opencontainers.image.revision="4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" +LABEL org.opencontainers.image.version="v0.5.2" VIASHDOCKER fi @@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_well_statistics v0.5.1" + echo "generate_well_statistics v0.5.2" exit ;; --input) @@ -838,7 +838,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.5.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.5.2' fi # print dockerfile diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index ecd3ef2e..32ab3532 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_eset" namespace: "eset" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -172,7 +172,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "r" @@ -198,11 +198,11 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +217,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index 6da72b12..b5c2f624 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -1,4 +1,4 @@ -// create_eset v0.5.1 +// create_eset v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_eset", "namespace" : "eset", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3036,7 +3036,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3072,12 +3072,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3094,7 +3094,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3947,7 +3947,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_eset", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_eset/nextflow.config b/target/nextflow/eset/create_eset/nextflow.config index 20207aa2..c61d3066 100644 --- a/target/nextflow/eset/create_eset/nextflow.config +++ b/target/nextflow/eset/create_eset/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_eset' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index 8039d60e..2caf0324 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_fdata" namespace: "eset" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -148,7 +148,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -177,11 +177,11 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -196,7 +196,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index 0120a6ff..1902261d 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -1,4 +1,4 @@ -// create_fdata v0.5.1 +// create_fdata v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_fdata", "namespace" : "eset", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3003,7 +3003,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3044,12 +3044,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3066,7 +3066,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3236,10 +3236,17 @@ def main(par): idx, cols = pd.factorize(column_to_get) symbol_values = annotation.reindex(cols, axis=1).to_numpy()[np.arange(len(annotation)), idx] annotation["SYMBOL"] = symbol_values - - logger.info("Writing to %s", par["output"]) + logger.info("Dropping unused columns") annotation = annotation.drop(["score", "source", "frame", "feature"], axis=1) + logger.info("Looking for duplicate rows and removing them. Starting with %i entries", annotation.shape[0]) + annotation = annotation.drop_duplicates(keep="first", ignore_index=True) + logger.info("After removing duplicates: %i entries", annotation.shape[0]) + logger.info("Writing to %s", par["output"]) annotation.to_csv(par["output"], sep="\\\\t", header=True, index=False, na_rep="NA") + # Do these checks *after* writing the csv in order to be able to check the data + logger.info("Checking for unique gene IDs") + if not annotation["gene_id"].is_unique: + raise ValueError("Values from the 'gene_id' column are not unique after processing!") logger.info("%s finished", meta['name']) @@ -3606,7 +3613,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_fdata", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_fdata/nextflow.config b/target/nextflow/eset/create_fdata/nextflow.config index 4f8edd55..9d66d737 100644 --- a/target/nextflow/eset/create_fdata/nextflow.config +++ b/target/nextflow/eset/create_fdata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_fdata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Create a fdata file\n' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index 74a7afdf..47c6393c 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pdata" namespace: "eset" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -191,11 +191,11 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -210,7 +210,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index b9f3ba01..c96b0aa7 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -1,4 +1,4 @@ -// create_pdata v0.5.1 +// create_pdata v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_pdata", "namespace" : "eset", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3017,7 +3017,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3058,12 +3058,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3080,7 +3080,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3553,7 +3553,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_pdata", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_pdata/nextflow.config b/target/nextflow/eset/create_pdata/nextflow.config index af839fd4..2253b172 100644 --- a/target/nextflow/eset/create_pdata/nextflow.config +++ b/target/nextflow/eset/create_pdata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_pdata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Create a pdata file by combining the mapping statistics \n' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 23f6b1bd..faacad06 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_eset" namespace: "integration_test_components/htrnaseq" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "r" @@ -148,11 +148,11 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -167,7 +167,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index 22902bb8..505559c9 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -1,4 +1,4 @@ -// check_eset v0.5.1 +// check_eset v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_eset", "namespace" : "integration_test_components/htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -2971,7 +2971,7 @@ meta = [ "id" : "docker", "image" : "bioconductor/bioconductor_docker:3.19", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -2997,12 +2997,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3019,7 +3019,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3646,7 +3646,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config index 33009d84..0460022a 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integration_test_components/htrnaseq/check_eset' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'This component test the ExpressionSet object as output by the main pipeline.' author = 'Dries Schaumont' } diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 8aab50bf..26303d35 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_cutadapt_output" namespace: "integration_test_components/well_demultiplexing" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -135,7 +135,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -158,11 +158,11 @@ build_info: output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -177,7 +177,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf index 051a672c..f6ab7937 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -1,4 +1,4 @@ -// check_cutadapt_output v0.5.1 +// check_cutadapt_output v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_cutadapt_output", "namespace" : "integration_test_components/well_demultiplexing", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -2978,7 +2978,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3009,12 +3009,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3031,7 +3031,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3527,7 +3527,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config index c655cd92..b8db0b0a 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integration_test_components/well_demultiplexing/check_cutadapt_output' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'This component test the cutadapt output from the well_demultiplex subworkflow.' author = 'Dries Schaumont' } diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index 24105524..926dab42 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_fastqs" namespace: "io" -version: "v0.5.1" +version: "v0.5.2" argument_groups: - name: "Input arguments" arguments: @@ -125,7 +125,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -143,11 +143,11 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -162,7 +162,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 6b52e243..5a41ae55 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -1,4 +1,4 @@ -// publish_fastqs v0.5.1 +// publish_fastqs v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish_fastqs", "namespace" : "io", - "version" : "v0.5.1", + "version" : "v0.5.2", "argument_groups" : [ { "name" : "Input arguments", @@ -2960,7 +2960,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -2983,12 +2983,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3005,7 +3005,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3440,7 +3440,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_fastqs", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_fastqs/nextflow.config b/target/nextflow/io/publish_fastqs/nextflow.config index d9fc3208..3db9d5e8 100644 --- a/target/nextflow/io/publish_fastqs/nextflow.config +++ b/target/nextflow/io/publish_fastqs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_fastqs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Publish the fastq files per well' } diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index 0fb90130..03b6a588 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_results" namespace: "io" -version: "v0.5.1" +version: "v0.5.2" argument_groups: - name: "Input arguments" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -187,11 +187,11 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -206,7 +206,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index a5e45180..47d711cd 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -1,4 +1,4 @@ -// publish_results v0.5.1 +// publish_results v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish_results", "namespace" : "io", - "version" : "v0.5.1", + "version" : "v0.5.2", "argument_groups" : [ { "name" : "Input arguments", @@ -3009,7 +3009,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3032,12 +3032,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3054,7 +3054,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3516,7 +3516,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_results", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_results/nextflow.config b/target/nextflow/io/publish_results/nextflow.config index c0232d8f..4573d855 100644 --- a/target/nextflow/io/publish_results/nextflow.config +++ b/target/nextflow/io/publish_results/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_results' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Publish the results' } diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index b02a145d..55224224 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "parallel_map" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -242,7 +242,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -298,7 +298,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 7cfd1668..7fcda21b 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -1,4 +1,4 @@ -// parallel_map v0.5.1 +// parallel_map v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "parallel_map", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3097,7 +3097,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3144,12 +3144,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3166,7 +3166,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3911,7 +3911,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/parallel_map", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/parallel_map/nextflow.config b/target/nextflow/parallel_map/nextflow.config index c80dca8e..23ede6ff 100644 --- a/target/nextflow/parallel_map/nextflow.config +++ b/target/nextflow/parallel_map/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'parallel_map' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n' author = 'Dries Schaumont, Toni Verbeiren' } diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 121a56fe..9d3cb0e6 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_report" namespace: "report" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -201,11 +201,11 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -220,7 +220,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index b7897b7c..cf896dc9 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -1,4 +1,4 @@ -// create_report v0.5.1 +// create_report v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_report", "namespace" : "report", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3016,7 +3016,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3077,12 +3077,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3099,7 +3099,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3561,7 +3561,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/report/create_report", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/create_report/nextflow.config b/target/nextflow/report/create_report/nextflow.config index 792c792a..a3c2d1ba 100644 --- a/target/nextflow/report/create_report/nextflow.config +++ b/target/nextflow/report/create_report/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'report/create_report' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Create a basic QC report in HTML format based on a number of esets.\n' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index 3b4c2b90..45dec916 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_star_logs" namespace: "stats" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -169,7 +169,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,11 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +217,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index 4dac78b1..8f50f1c8 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -1,4 +1,4 @@ -// combine_star_logs v0.5.1 +// combine_star_logs v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_star_logs", "namespace" : "stats", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3019,7 +3019,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3060,12 +3060,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3082,7 +3082,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3718,7 +3718,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/combine_star_logs", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/combine_star_logs/nextflow.config b/target/nextflow/stats/combine_star_logs/nextflow.config index 9a72fa69..ec6cba79 100644 --- a/target/nextflow/stats/combine_star_logs/nextflow.config +++ b/target/nextflow/stats/combine_star_logs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/combine_star_logs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' author = 'Dries Schaumont' } diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index e2047f1b..a3e74f80 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_pool_statistics" namespace: "stats" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "apt" @@ -182,11 +182,11 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -201,7 +201,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 140dc211..ce116218 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -1,4 +1,4 @@ -// generate_pool_statistics v0.5.1 +// generate_pool_statistics v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_pool_statistics", "namespace" : "stats", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3003,7 +3003,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3044,12 +3044,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3066,7 +3066,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3567,7 +3567,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_pool_statistics", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_pool_statistics/nextflow.config b/target/nextflow/stats/generate_pool_statistics/nextflow.config index e7877bdb..599834b6 100644 --- a/target/nextflow/stats/generate_pool_statistics/nextflow.config +++ b/target/nextflow/stats/generate_pool_statistics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/generate_pool_statistics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index 20b2fa96..9ac8a435 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_well_statistics" namespace: "stats" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.1" + target_tag: "v0.5.2" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,11 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -283,7 +283,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index 2bc5272c..20870318 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -1,4 +1,4 @@ -// generate_well_statistics v0.5.1 +// generate_well_statistics v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_well_statistics", "namespace" : "stats", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3084,7 +3084,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.1", + "target_tag" : "v0.5.2", "namespace_separator" : "/", "setup" : [ { @@ -3139,12 +3139,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3161,7 +3161,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", @@ -3658,7 +3658,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_well_statistics", - "tag" : "v0.5.1" + "tag" : "v0.5.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_well_statistics/nextflow.config b/target/nextflow/stats/generate_well_statistics/nextflow.config index baa832b0..cbfa0325 100644 --- a/target/nextflow/stats/generate_well_statistics/nextflow.config +++ b/target/nextflow/stats/generate_well_statistics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/generate_well_statistics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Generate summary statistics from BAM files generated by STAR solo.' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index e9b6c755..5559d74d 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "listInputDir" namespace: "utils" -version: "v0.5.1" +version: "v0.5.2" argument_groups: - name: "Arguments" arguments: @@ -165,11 +165,11 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -184,7 +184,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index a3e052f5..67d1194f 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -1,4 +1,4 @@ -// listInputDir v0.5.1 +// listInputDir v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "listInputDir", "namespace" : "utils", - "version" : "v0.5.1", + "version" : "v0.5.2", "argument_groups" : [ { "name" : "Arguments", @@ -3004,12 +3004,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3026,7 +3026,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/utils/listInputDir/nextflow.config b/target/nextflow/utils/listInputDir/nextflow.config index da4c0747..e3718c5b 100644 --- a/target/nextflow/utils/listInputDir/nextflow.config +++ b/target/nextflow/utils/listInputDir/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/listInputDir' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'List the contents of a directory and parse contained fastq files' } diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index fe049b38..2bdbef24 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htrnaseq" namespace: "workflows" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -319,7 +319,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/stats/combine_star_logs" @@ -334,7 +334,7 @@ build_info: - "target/nextflow/report/create_report" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -349,7 +349,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index ff0fd677..175235e4 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -1,4 +1,4 @@ -// htrnaseq v0.5.1 +// htrnaseq v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "htrnaseq", "namespace" : "workflows", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3223,12 +3223,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3245,7 +3245,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/htrnaseq/nextflow.config b/target/nextflow/workflows/htrnaseq/nextflow.config index a90993f6..5c8c8af6 100644 --- a/target/nextflow/workflows/htrnaseq/nextflow.config +++ b/target/nextflow/workflows/htrnaseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/htrnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index 4a8e6502..d804d006 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "runner" namespace: "workflows" -version: "v0.5.1" +version: "v0.5.2" argument_groups: - name: "Input arguments" arguments: @@ -207,7 +207,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/utils/listInputDir" @@ -216,7 +216,7 @@ build_info: - "target/nextflow/io/publish_results" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -231,7 +231,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index 4da31fb6..4c1e644a 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.5.1 +// runner v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "runner", "namespace" : "workflows", - "version" : "v0.5.1", + "version" : "v0.5.2", "argument_groups" : [ { "name" : "Input arguments", @@ -3069,12 +3069,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3091,7 +3091,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config index fb845658..264ed62c 100644 --- a/target/nextflow/workflows/runner/nextflow.config +++ b/target/nextflow/workflows/runner/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/runner' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Runner for HT RNA-seq pipeline' } diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 5ae986d9..4dfbd25e 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_demultiplex" namespace: "workflows" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -211,14 +211,14 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt" - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -233,7 +233,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index d32496b5..06e52f78 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -1,4 +1,4 @@ -// well_demultiplex v0.5.1 +// well_demultiplex v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_demultiplex", "namespace" : "workflows", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3084,12 +3084,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3106,7 +3106,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_demultiplex/nextflow.config b/target/nextflow/workflows/well_demultiplex/nextflow.config index 3355daa4..1a5ca876 100644 --- a/target/nextflow/workflows/well_demultiplex/nextflow.config +++ b/target/nextflow/workflows/well_demultiplex/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_demultiplex' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' description = 'Demultiplexing on well level' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index 7044dd8b..e1fb2eec 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_metadata" namespace: "workflows" -version: "v0.5.1" +version: "v0.5.2" authors: - name: "Dries Schaumont" roles: @@ -209,11 +209,11 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.0" - git_commit: "73afe64a7776924434bdf6e66dee26f2f6c6246d" + git_commit: "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.5.1" + version: "v0.5.2" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -228,7 +228,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index b143641e..d7c66dca 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -1,4 +1,4 @@ -// well_metadata v0.5.1 +// well_metadata v0.5.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_metadata", "namespace" : "workflows", - "version" : "v0.5.1", + "version" : "v0.5.2", "authors" : [ { "name" : "Dries Schaumont", @@ -3064,12 +3064,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.0", - "git_commit" : "73afe64a7776924434bdf6e66dee26f2f6c6246d", + "git_commit" : "4e7d7f7cd26be6e00fb50d9aaadb8d315640f24f", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.1", + "version" : "v0.5.2", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3086,7 +3086,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.1'" + ".engines[.type == 'docker'].target_tag := 'v0.5.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_metadata/nextflow.config b/target/nextflow/workflows/well_metadata/nextflow.config index b6cb7448..2b336e73 100644 --- a/target/nextflow/workflows/well_metadata/nextflow.config +++ b/target/nextflow/workflows/well_metadata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_metadata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.1' + version = 'v0.5.2' author = 'Dries Schaumont' }