diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e20fec0..937185a6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,16 @@ +# htrnaseq v0.14.3 + +## Bug fixes + +* `parallel_map`: detection of gzip compressed files now works if the file inadvertently also matches another file type (PR #94). + +# Minor changes + +* Change `cutadapt`'s memory label from `highmem` to `midmem` (PR #93). + # htrnaseq v0.14.2 -# Bug fixes +## Bug fixes * Fix esets not being created when processing multiple samples from a single run (PR #92). @@ -8,23 +18,23 @@ # htrnaseq v0.14.1 -# Minor changes +## Minor changes * FASTQ files are now gzip compressed (PR #88). * Bump biobox to `v0.4.2` and craftbox to `v0.3.1` (PR #88). -# Bug fixes +## Bug fixes * Fix an issue where samples with the same experiment ID but from different projects were concatenated (PR #87). # htrnaseq v0.14.0 -# Major changes +## Major changes * `runner`: major refactor that allows sequencing runs to be only demultiplexed once (PR #85). -# Minor changes +## Minor changes * `generate_well_statistics`: increase memory requirements from `verylowmem` to `lowmem` (PR #86). diff --git a/_viash.yaml b/_viash.yaml index 73712652..3974d09a 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/src/parallel_map/script.sh b/src/parallel_map/script.sh index a2c489b0..caf190a5 100755 --- a/src/parallel_map/script.sh +++ b/src/parallel_map/script.sh @@ -169,7 +169,9 @@ function _run() { function is_gzipped { printf "Checking if input '$1' (barcode '$barcode') is gzipped... " - if file "$1" | grep -q 'gzip'; then + # The file might match more than one mime-type, but if the `-k` flag is not + # set, file will only output one. + if file --mime-type -k "$1" | grep -q 'gzip'; then echo "Done, detected compressed file." return fi diff --git a/src/workflows/well_demultiplex/main.nf b/src/workflows/well_demultiplex/main.nf index 008cba94..0d18bccf 100644 --- a/src/workflows/well_demultiplex/main.nf +++ b/src/workflows/well_demultiplex/main.nf @@ -51,7 +51,7 @@ workflow run_wf { } } | cutadapt.run( - directives: [label: ["highmem", "midcpu"]], + directives: [label: ["midmem", "midcpu"]], fromState: { id, state -> [ input: state.input_r1, diff --git a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml index 172c0175..05c903b4 100644 --- a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "listInputDir" namespace: "utils" -version: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Arguments" arguments: @@ -169,11 +169,11 @@ build_info: output: "target/_private/nextflow/utils/listInputDir" executable: "target/_private/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -205,7 +205,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/_private/nextflow/utils/listInputDir/_viash.yaml b/target/_private/nextflow/utils/listInputDir/_viash.yaml index 73712652..3974d09a 100644 --- a/target/_private/nextflow/utils/listInputDir/_viash.yaml +++ b/target/_private/nextflow/utils/listInputDir/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/_private/nextflow/utils/listInputDir/main.nf b/target/_private/nextflow/utils/listInputDir/main.nf index 625563dd..7ad7dfc8 100644 --- a/target/_private/nextflow/utils/listInputDir/main.nf +++ b/target/_private/nextflow/utils/listInputDir/main.nf @@ -1,4 +1,4 @@ -// listInputDir v0.14.2 +// listInputDir v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "listInputDir", "namespace" : "utils", - "version" : "v0.14.2", + "version" : "v0.14.3", "argument_groups" : [ { "name" : "Arguments", @@ -3236,12 +3236,12 @@ meta = [ "engine" : "native|native", "output" : "target/_private/nextflow/utils/listInputDir", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3259,7 +3259,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/_private/nextflow/utils/listInputDir/nextflow.config b/target/_private/nextflow/utils/listInputDir/nextflow.config index dc22099b..d666896b 100644 --- a/target/_private/nextflow/utils/listInputDir/nextflow.config +++ b/target/_private/nextflow/utils/listInputDir/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/listInputDir' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.2' + version = 'v0.14.3' description = 'List the contents of a directory and parse contained fastq files' } diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml b/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml index 80709d0f..8ce27621 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_fastqs_to_esets" namespace: "workflows" -version: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -313,7 +313,7 @@ build_info: output: "target/_private/nextflow/workflows/well_fastqs_to_esets" executable: "target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/stats/combine_star_logs" @@ -330,7 +330,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -362,7 +362,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml b/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml index 73712652..3974d09a 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf b/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf index 1c4f6556..c15a8ab0 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf @@ -1,4 +1,4 @@ -// well_fastqs_to_esets v0.14.2 +// well_fastqs_to_esets v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_fastqs_to_esets", "namespace" : "workflows", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3444,12 +3444,12 @@ meta = [ "engine" : "native|native", "output" : "target/_private/nextflow/workflows/well_fastqs_to_esets", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3467,7 +3467,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config b/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config index a566b379..c41b74e6 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_fastqs_to_esets' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.2' + version = 'v0.14.3' description = 'Map a list of FASTQ files (one for each well) to a reference genome and generate count matrices.\nSometimes counts from different FASTQ files need to be concatenated. This is done bases on the sample_id:\nif the sample ID of the two plates are identical, the FASTQ files will we joined _before_ mapping.\n' author = 'Dries Schaumont' } diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 0cbfecf8..53cd4c1c 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "r" @@ -206,11 +206,11 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -242,7 +242,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_eset/_viash.yaml b/target/executable/eset/create_eset/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/eset/create_eset/_viash.yaml +++ b/target/executable/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index 671f7708..bf9f339f 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 v0.14.2 +# create_eset v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -456,10 +456,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR 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="2025-11-27T08:38:31Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:50Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_eset v0.14.2" + echo "create_eset v0.14.3" echo "" echo "Arguments:" echo " --pDataFile" @@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_eset v0.14.2" + echo "create_eset v0.14.3" exit ;; --pDataFile) @@ -794,7 +794,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.3' fi # print dockerfile diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index fd135f47..588b9777 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -154,7 +154,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -183,11 +183,11 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -219,7 +219,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_fdata/_viash.yaml b/target/executable/eset/create_fdata/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/eset/create_fdata/_viash.yaml +++ b/target/executable/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index f97e7bfd..43542afe 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 v0.14.2 +# create_fdata v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_fdata v0.14.2" + echo "create_fdata v0.14.3" echo "" echo "Create a fdata file" echo "" @@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_fdata v0.14.2" + echo "create_fdata v0.14.3" exit ;; --gtf) @@ -756,7 +756,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.3' fi # print dockerfile diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 6f725b8b..3262fafa 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -168,7 +168,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -197,11 +197,11 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -233,7 +233,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_pdata/_viash.yaml b/target/executable/eset/create_pdata/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/eset/create_pdata/_viash.yaml +++ b/target/executable/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index 994d764d..7607e3ae 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 v0.14.2 +# create_pdata v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-11-27T08:38:31Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pdata v0.14.2" + echo "create_pdata v0.14.3" echo "" echo "Create a pdata file by combining the mapping statistics" echo "" @@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pdata v0.14.2" + echo "create_pdata v0.14.3" exit ;; --star_stats_file) @@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.3' 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 f13be2d3..0bcb2e7a 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -134,7 +134,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "r" @@ -155,11 +155,11 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -191,7 +191,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 0294ebf5..f7b0cf78 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 v0.14.2 +# check_eset v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -455,10 +455,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR 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="2025-11-27T08:38:33Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_eset v0.14.2" + echo "check_eset v0.14.3" echo "" echo "This component test the ExpressionSet object as output by the main pipeline." echo "" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_eset v0.14.2" + echo "check_eset v0.14.3" exit ;; --eset) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.3' 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 a842176f..03953861 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -164,11 +164,11 @@ 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: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -200,7 +200,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 ec7a5f06..ff52ad65 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 v0.14.2 +# check_cutadapt_output v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="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="2025-11-27T08:38:33Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_cutadapt_output v0.14.2" + echo "check_cutadapt_output v0.14.3" echo "" echo "This component test the cutadapt output from the well_demultiplex subworkflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_cutadapt_output v0.14.2" + echo "check_cutadapt_output v0.14.3" exit ;; --fastq_r1) @@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.3' fi # print dockerfile diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 187cddcb..891e4060 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: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Input arguments" arguments: @@ -121,7 +121,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -139,11 +139,11 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -175,7 +175,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_fastqs/_viash.yaml b/target/executable/io/publish_fastqs/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/io/publish_fastqs/_viash.yaml +++ b/target/executable/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index 48855eab..af93958f 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 v0.14.2 +# publish_fastqs v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_fastqs v0.14.2" + echo "publish_fastqs v0.14.3" echo "" echo "Publish the fastq files per well" echo "" @@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_fastqs v0.14.2" + echo "publish_fastqs v0.14.3" exit ;; --input) @@ -750,7 +750,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.3' fi # print dockerfile diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 8ad4baa7..39f9ba1f 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: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Input arguments" arguments: @@ -261,7 +261,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -315,7 +315,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_results/_viash.yaml b/target/executable/io/publish_results/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/io/publish_results/_viash.yaml +++ b/target/executable/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index caf9afad..fa31ffd1 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 v0.14.2 +# publish_results v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-11-27T08:38:33Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_results v0.14.2" + echo "publish_results v0.14.3" echo "" echo "Publish the results" echo "" @@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_results v0.14.2" + echo "publish_results v0.14.3" exit ;; --star_output) @@ -986,7 +986,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.3' fi # print dockerfile diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 41a090cc..99dad21a 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -285,11 +285,11 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -321,7 +321,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/parallel_map/_viash.yaml b/target/executable/parallel_map/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/parallel_map/_viash.yaml +++ b/target/executable/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index 46cc7ddf..cebcc90b 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 v0.14.2 +# parallel_map v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -461,10 +461,10 @@ 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="2025-11-27T08:38:33Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "parallel_map v0.14.2" + echo "parallel_map v0.14.3" echo "" echo "Map wells in batch, using STAR" echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin" @@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "parallel_map v0.14.2" + echo "parallel_map v0.14.3" exit ;; --input_r1) @@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.3' fi # print dockerfile @@ -1502,7 +1502,9 @@ function _run() { function is_gzipped { printf "Checking if input '\$1' (barcode '\$barcode') is gzipped... " - if file "\$1" | grep -q 'gzip'; then + # The file might match more than one mime-type, but if the \`-k\` flag is not + # set, file will only output one. + if file --mime-type -k "\$1" | grep -q 'gzip'; then echo "Done, detected compressed file." return fi diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 66aaf76b..dde809a1 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -215,11 +215,11 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -251,7 +251,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/report/create_report/_viash.yaml b/target/executable/report/create_report/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/report/create_report/_viash.yaml +++ b/target/executable/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 67ed50bb..b1873288 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 v0.14.2 +# create_report v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -465,10 +465,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR 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="2025-11-27T08:38:33Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:50Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_report v0.14.2" + echo "create_report v0.14.3" echo "" echo "Create a basic QC report in HTML format based on a number of esets." echo "" @@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_report v0.14.2" + echo "create_report v0.14.3" exit ;; --eset) @@ -763,7 +763,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.3' 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 2e92c121..81984d3c 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -175,7 +175,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -204,11 +204,11 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -240,7 +240,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/combine_star_logs/_viash.yaml b/target/executable/stats/combine_star_logs/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/stats/combine_star_logs/_viash.yaml +++ b/target/executable/stats/combine_star_logs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 0ebdf0ca..2dd2ad7b 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 v0.14.2 +# combine_star_logs v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:50Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "combine_star_logs v0.14.2" + echo "combine_star_logs v0.14.3" echo "" echo "Arguments:" echo " --barcodes" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "combine_star_logs v0.14.2" + echo "combine_star_logs v0.14.3" exit ;; --barcodes) @@ -825,7 +825,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.3' 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 0b178111..8c467abb 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -188,11 +188,11 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -224,7 +224,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_pool_statistics/_viash.yaml b/target/executable/stats/generate_pool_statistics/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/stats/generate_pool_statistics/_viash.yaml +++ b/target/executable/stats/generate_pool_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 82bd83e8..2f790bb9 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 v0.14.2 +# generate_pool_statistics v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_pool_statistics v0.14.2" + echo "generate_pool_statistics v0.14.3" echo "" echo "Arguments:" echo " --nrReadsNrGenesPerChrom" @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_pool_statistics v0.14.2" + echo "generate_pool_statistics v0.14.3" exit ;; --nrReadsNrGenesPerChrom) @@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.3' 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 ac8d8194..9cd31c25 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -230,7 +230,7 @@ engines: id: "docker" image: "python:3.13-trixie" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -260,11 +260,11 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -296,7 +296,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_well_statistics/_viash.yaml b/target/executable/stats/generate_well_statistics/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/stats/generate_well_statistics/_viash.yaml +++ b/target/executable/stats/generate_well_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index fbc96900..64c0bca8 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 v0.14.2 +# generate_well_statistics v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:52Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_well_statistics v0.14.2" + echo "generate_well_statistics v0.14.3" echo "" echo "Generate summary statistics from BAM files generated by STAR solo." echo "" @@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_well_statistics v0.14.2" + echo "generate_well_statistics v0.14.3" exit ;; --input) @@ -861,7 +861,7 @@ if [[ "$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:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.3' fi # print dockerfile diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml index bd7d004b..6bbf1eef 100644 --- a/target/executable/utils/save_params/.config.vsh.yaml +++ b/target/executable/utils/save_params/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "save_params" namespace: "utils" -version: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Inputs" arguments: @@ -128,7 +128,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -151,11 +151,11 @@ build_info: output: "target/executable/utils/save_params" executable: "target/executable/utils/save_params/save_params" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -187,7 +187,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/utils/save_params/_viash.yaml b/target/executable/utils/save_params/_viash.yaml index 73712652..3974d09a 100644 --- a/target/executable/utils/save_params/_viash.yaml +++ b/target/executable/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params index 11769d56..5ba76403 100755 --- a/target/executable/utils/save_params/save_params +++ b/target/executable/utils/save_params/save_params @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# save_params v0.14.2 +# save_params v0.14.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "pyyaml" LABEL org.opencontainers.image.description="Companion container for running component utils save_params" -LABEL org.opencontainers.image.created="2025-11-27T08:38:32Z" +LABEL org.opencontainers.image.created="2025-12-03T14:02:51Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="40230f83eef0c6488e3bc664b535e10f77ddfacb" -LABEL org.opencontainers.image.version="v0.14.2" +LABEL org.opencontainers.image.revision="e9507042c57fcbf9a03d769d758d5d36e1631d25" +LABEL org.opencontainers.image.version="v0.14.3" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "save_params v0.14.2" + echo "save_params v0.14.3" echo "" echo "Save parameters to a YAML file" echo "" @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "save_params v0.14.2" + echo "save_params v0.14.3" exit ;; --id) @@ -763,7 +763,7 @@ if [[ "$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/utils/save_params:v0.14.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.3' fi # print dockerfile diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index f7544030..0fdcec7c 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "r" @@ -206,11 +206,11 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -242,7 +242,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_eset/_viash.yaml b/target/nextflow/eset/create_eset/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/eset/create_eset/_viash.yaml +++ b/target/nextflow/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index 8703719e..4d63394c 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -1,4 +1,4 @@ -// create_eset v0.14.2 +// create_eset v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_eset", "namespace" : "eset", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3271,7 +3271,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3309,12 +3309,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3332,7 +3332,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -4207,7 +4207,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_eset", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_eset/nextflow.config b/target/nextflow/eset/create_eset/nextflow.config index 0e3ab0eb..51c12444 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 = 'v0.14.2' + version = 'v0.14.3' 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 61fbba62..44aab8fd 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -154,7 +154,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -183,11 +183,11 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -219,7 +219,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_fdata/_viash.yaml b/target/nextflow/eset/create_fdata/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/eset/create_fdata/_viash.yaml +++ b/target/nextflow/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index dff57eac..ed2dbe07 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -1,4 +1,4 @@ -// create_fdata v0.14.2 +// create_fdata v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_fdata", "namespace" : "eset", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3279,12 +3279,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3302,7 +3302,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3872,7 +3872,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_fdata", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_fdata/nextflow.config b/target/nextflow/eset/create_fdata/nextflow.config index 5c2a6b98..5e3f264f 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 = 'v0.14.2' + version = 'v0.14.3' 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 27ade465..7e9c7c36 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -168,7 +168,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -197,11 +197,11 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -233,7 +233,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_pdata/_viash.yaml b/target/nextflow/eset/create_pdata/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/eset/create_pdata/_viash.yaml +++ b/target/nextflow/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index 38687e91..2b245bdc 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -1,4 +1,4 @@ -// create_pdata v0.14.2 +// create_pdata v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_pdata", "namespace" : "eset", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3252,7 +3252,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3293,12 +3293,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3316,7 +3316,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3812,7 +3812,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_pdata", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_pdata/nextflow.config b/target/nextflow/eset/create_pdata/nextflow.config index b2360af1..d8a14ec2 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 = 'v0.14.2' + version = 'v0.14.3' 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 4bf51444..68113c75 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -134,7 +134,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "r" @@ -155,11 +155,11 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -191,7 +191,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 cfbc6b7e..8b593b69 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 v0.14.2 +// check_eset v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_eset", "namespace" : "integration_test_components/htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3206,7 +3206,7 @@ meta = [ "id" : "docker", "image" : "bioconductor/bioconductor_docker:3.19", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3233,12 +3233,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3256,7 +3256,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3906,7 +3906,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "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 b783b1f9..d913da87 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 = 'v0.14.2' + version = 'v0.14.3' 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 9821b05e..54a096ad 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -164,11 +164,11 @@ 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: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -200,7 +200,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 e6e9f84a..acb33180 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 v0.14.2 +// check_cutadapt_output v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_cutadapt_output", "namespace" : "integration_test_components/well_demultiplexing", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3213,7 +3213,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3244,12 +3244,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3267,7 +3267,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3786,7 +3786,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "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 0c8acbe5..cb21f593 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 = 'v0.14.2' + version = 'v0.14.3' 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 822428d8..9c259a74 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: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Input arguments" arguments: @@ -121,7 +121,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -139,11 +139,11 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -175,7 +175,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_fastqs/_viash.yaml b/target/nextflow/io/publish_fastqs/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/io/publish_fastqs/_viash.yaml +++ b/target/nextflow/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 99394d17..9ffdec0a 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -1,4 +1,4 @@ -// publish_fastqs v0.14.2 +// publish_fastqs v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish_fastqs", "namespace" : "io", - "version" : "v0.14.2", + "version" : "v0.14.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3184,7 +3184,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3207,12 +3207,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3230,7 +3230,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3682,7 +3682,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_fastqs", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_fastqs/nextflow.config b/target/nextflow/io/publish_fastqs/nextflow.config index c59ae79e..6cf94edb 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 = 'v0.14.2' + version = 'v0.14.3' 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 20e1a3e2..c8fe0c23 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: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Input arguments" arguments: @@ -261,7 +261,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -315,7 +315,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_results/_viash.yaml b/target/nextflow/io/publish_results/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/io/publish_results/_viash.yaml +++ b/target/nextflow/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index d100ba5c..7eb9f1de 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -1,4 +1,4 @@ -// publish_results v0.14.2 +// publish_results v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish_results", "namespace" : "io", - "version" : "v0.14.2", + "version" : "v0.14.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3346,7 +3346,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3369,12 +3369,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3392,7 +3392,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3909,7 +3909,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_results", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_results/nextflow.config b/target/nextflow/io/publish_results/nextflow.config index c6266fa3..22fd1d0f 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 = 'v0.14.2' + version = 'v0.14.3' description = 'Publish the results' } diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index d6101735..3d3755e9 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -285,11 +285,11 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -321,7 +321,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/parallel_map/_viash.yaml b/target/nextflow/parallel_map/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/parallel_map/_viash.yaml +++ b/target/nextflow/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 9a9ae823..e0468dc9 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -1,4 +1,4 @@ -// parallel_map v0.14.2 +// parallel_map v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "parallel_map", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3332,7 +3332,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3379,12 +3379,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3402,7 +3402,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3624,7 +3624,9 @@ function _run() { function is_gzipped { printf "Checking if input '\\$1' (barcode '\\$barcode') is gzipped... " - if file "\\$1" | grep -q 'gzip'; then + # The file might match more than one mime-type, but if the \\`-k\\` flag is not + # set, file will only output one. + if file --mime-type -k "\\$1" | grep -q 'gzip'; then echo "Done, detected compressed file." return fi @@ -4171,7 +4173,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/parallel_map", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/parallel_map/nextflow.config b/target/nextflow/parallel_map/nextflow.config index 392f1002..1974fb9a 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 = 'v0.14.2' + version = 'v0.14.3' 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 a5eeb95c..a2bfe344 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -215,11 +215,11 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -251,7 +251,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/report/create_report/_viash.yaml b/target/nextflow/report/create_report/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/report/create_report/_viash.yaml +++ b/target/nextflow/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index 1c6c4ae8..ccd54b88 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -1,4 +1,4 @@ -// create_report v0.14.2 +// create_report v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_report", "namespace" : "report", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3251,7 +3251,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3323,12 +3323,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3346,7 +3346,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3831,7 +3831,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/report/create_report", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/create_report/nextflow.config b/target/nextflow/report/create_report/nextflow.config index e2cc588e..acbf351c 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 = 'v0.14.2' + version = 'v0.14.3' 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 c4dd1dea..a3ae7958 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -175,7 +175,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -204,11 +204,11 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -240,7 +240,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/combine_star_logs/_viash.yaml b/target/nextflow/stats/combine_star_logs/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/stats/combine_star_logs/_viash.yaml +++ b/target/nextflow/stats/combine_star_logs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index 59790ab8..80129deb 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 v0.14.2 +// combine_star_logs v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_star_logs", "namespace" : "stats", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3254,7 +3254,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3295,12 +3295,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3318,7 +3318,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3977,7 +3977,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/combine_star_logs", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/combine_star_logs/nextflow.config b/target/nextflow/stats/combine_star_logs/nextflow.config index 221ffaf2..a548c354 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 = 'v0.14.2' + version = 'v0.14.3' 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 3e6a80d8..3fd496f6 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -188,11 +188,11 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -224,7 +224,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_pool_statistics/_viash.yaml b/target/nextflow/stats/generate_pool_statistics/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/stats/generate_pool_statistics/_viash.yaml +++ b/target/nextflow/stats/generate_pool_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 4b3a0b5b..3f3177b1 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 v0.14.2 +// generate_pool_statistics v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_pool_statistics", "namespace" : "stats", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3279,12 +3279,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3302,7 +3302,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3832,7 +3832,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_pool_statistics", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_pool_statistics/nextflow.config b/target/nextflow/stats/generate_pool_statistics/nextflow.config index 29d77c27..eb3aeaa6 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 = 'v0.14.2' + version = 'v0.14.3' 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 c95c9e98..683b340f 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -230,7 +230,7 @@ engines: id: "docker" image: "python:3.13-trixie" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -260,11 +260,11 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -296,7 +296,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_well_statistics/_viash.yaml b/target/nextflow/stats/generate_well_statistics/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/stats/generate_well_statistics/_viash.yaml +++ b/target/nextflow/stats/generate_well_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index 6dbb1d3f..645b0d19 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 v0.14.2 +// generate_well_statistics v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_well_statistics", "namespace" : "stats", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3319,7 +3319,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-trixie", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3361,12 +3361,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3384,7 +3384,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3905,7 +3905,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_well_statistics", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_well_statistics/nextflow.config b/target/nextflow/stats/generate_well_statistics/nextflow.config index 07049506..a989aadc 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 = 'v0.14.2' + version = 'v0.14.3' description = 'Generate summary statistics from BAM files generated by STAR solo.' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml index d173173c..aa6e89aa 100644 --- a/target/nextflow/utils/concatRuns/.config.vsh.yaml +++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "concatRuns" namespace: "utils" -version: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Arguments" arguments: @@ -160,13 +160,13 @@ build_info: output: "target/nextflow/utils/concatRuns" executable: "target/nextflow/utils/concatRuns/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/craftbox/v0.3.1/nextflow/concat_text" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -198,7 +198,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/concatRuns/_viash.yaml b/target/nextflow/utils/concatRuns/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/utils/concatRuns/_viash.yaml +++ b/target/nextflow/utils/concatRuns/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf index 44ba347a..b0ada6be 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -1,4 +1,4 @@ -// concatRuns v0.14.2 +// concatRuns v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "concatRuns", "namespace" : "utils", - "version" : "v0.14.2", + "version" : "v0.14.3", "argument_groups" : [ { "name" : "Arguments", @@ -3229,12 +3229,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3252,7 +3252,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/utils/concatRuns/nextflow.config b/target/nextflow/utils/concatRuns/nextflow.config index aaa7c302..8e77cb41 100644 --- a/target/nextflow/utils/concatRuns/nextflow.config +++ b/target/nextflow/utils/concatRuns/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/concatRuns' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.2' + version = 'v0.14.3' description = 'Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n' } diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml index 5731a5bb..c3b63cd7 100644 --- a/target/nextflow/utils/save_params/.config.vsh.yaml +++ b/target/nextflow/utils/save_params/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "save_params" namespace: "utils" -version: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Inputs" arguments: @@ -128,7 +128,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.2" + target_tag: "v0.14.3" namespace_separator: "/" setup: - type: "apt" @@ -151,11 +151,11 @@ build_info: output: "target/nextflow/utils/save_params" executable: "target/nextflow/utils/save_params/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -187,7 +187,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/save_params/_viash.yaml b/target/nextflow/utils/save_params/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/utils/save_params/_viash.yaml +++ b/target/nextflow/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf index 9830d37a..27a046eb 100644 --- a/target/nextflow/utils/save_params/main.nf +++ b/target/nextflow/utils/save_params/main.nf @@ -1,4 +1,4 @@ -// save_params v0.14.2 +// save_params v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "save_params", "namespace" : "utils", - "version" : "v0.14.2", + "version" : "v0.14.3", "argument_groups" : [ { "name" : "Inputs", @@ -3192,7 +3192,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.2", + "target_tag" : "v0.14.3", "namespace_separator" : "/", "setup" : [ { @@ -3223,12 +3223,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/utils/save_params", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3246,7 +3246,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3711,7 +3711,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/utils/save_params", - "tag" : "v0.14.2" + "tag" : "v0.14.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/utils/save_params/nextflow.config b/target/nextflow/utils/save_params/nextflow.config index 4a82a117..d598c37c 100644 --- a/target/nextflow/utils/save_params/nextflow.config +++ b/target/nextflow/utils/save_params/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/save_params' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.2' + version = 'v0.14.3' description = 'Save parameters to a YAML file\n' } diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index 68366735..88181ab1 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -326,7 +326,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/workflows/well_demultiplex" @@ -334,7 +334,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -366,7 +366,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/htrnaseq/_viash.yaml b/target/nextflow/workflows/htrnaseq/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/workflows/htrnaseq/_viash.yaml +++ b/target/nextflow/workflows/htrnaseq/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index 9a5ec74b..b6c75865 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -1,4 +1,4 @@ -// htrnaseq v0.14.2 +// htrnaseq v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "htrnaseq", "namespace" : "workflows", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3442,12 +3442,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3465,7 +3465,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/htrnaseq/nextflow.config b/target/nextflow/workflows/htrnaseq/nextflow.config index 7a28f322..98e2c9a7 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 = 'v0.14.2' + version = 'v0.14.3' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index d233a8d9..857f3c8d 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: "v0.14.2" +version: "v0.14.3" argument_groups: - name: "Input arguments" arguments: @@ -337,7 +337,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/_private/nextflow/utils/listInputDir" @@ -348,7 +348,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -380,7 +380,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/runner/_viash.yaml b/target/nextflow/workflows/runner/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/workflows/runner/_viash.yaml +++ b/target/nextflow/workflows/runner/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index 3f653d66..11f21707 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.14.2 +// runner v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "runner", "namespace" : "workflows", - "version" : "v0.14.2", + "version" : "v0.14.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3452,12 +3452,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3475,7 +3475,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config index 7daa5af2..0c7ccf39 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 = 'v0.14.2' + version = 'v0.14.3' 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 8bee0ee9..efd92e27 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -222,7 +222,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.4.2/nextflow/cutadapt" @@ -230,7 +230,7 @@ build_info: - "target/dependencies/vsh/vsh/craftbox/v0.3.1/nextflow/move_files_to_directory" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -262,7 +262,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_demultiplex/_viash.yaml b/target/nextflow/workflows/well_demultiplex/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/workflows/well_demultiplex/_viash.yaml +++ b/target/nextflow/workflows/well_demultiplex/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index 2230776c..dcfec674 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -1,4 +1,4 @@ -// well_demultiplex v0.14.2 +// well_demultiplex v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_demultiplex", "namespace" : "workflows", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3327,12 +3327,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3350,7 +3350,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", @@ -3433,7 +3433,7 @@ workflow run_wf { } } | cutadapt.run( - directives: [label: ["highmem", "midcpu"]], + directives: [label: ["midmem", "midcpu"]], fromState: { id, state -> [ input: state.input_r1, diff --git a/target/nextflow/workflows/well_demultiplex/nextflow.config b/target/nextflow/workflows/well_demultiplex/nextflow.config index c7ac23f0..cd3d3760 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 = 'v0.14.2' + version = 'v0.14.3' 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 74cf833c..b27fbc35 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: "v0.14.2" +version: "v0.14.3" authors: - name: "Dries Schaumont" roles: @@ -215,11 +215,11 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.4" - git_commit: "40230f83eef0c6488e3bc664b535e10f77ddfacb" + git_commit: "e9507042c57fcbf9a03d769d758d5d36e1631d25" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.2" + version: "v0.14.3" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -251,7 +251,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.3'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_metadata/_viash.yaml b/target/nextflow/workflows/well_metadata/_viash.yaml index 73712652..3974d09a 100644 --- a/target/nextflow/workflows/well_metadata/_viash.yaml +++ b/target/nextflow/workflows/well_metadata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.2 +version: v0.14.3 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index b7c3710e..c0fdb9b6 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -1,4 +1,4 @@ -// well_metadata v0.14.2 +// well_metadata v0.14.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_metadata", "namespace" : "workflows", - "version" : "v0.14.2", + "version" : "v0.14.3", "authors" : [ { "name" : "Dries Schaumont", @@ -3299,12 +3299,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.4", - "git_commit" : "40230f83eef0c6488e3bc664b535e10f77ddfacb", + "git_commit" : "e9507042c57fcbf9a03d769d758d5d36e1631d25", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.2", + "version" : "v0.14.3", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3322,7 +3322,7 @@ 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.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.14.2'" + ".engines[.type == 'docker'].target_tag := 'v0.14.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_metadata/nextflow.config b/target/nextflow/workflows/well_metadata/nextflow.config index 5ec44980..e200a2e2 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 = 'v0.14.2' + version = 'v0.14.3' author = 'Dries Schaumont' }