From c7c4845b305ba04ac7d2b0539b56093447d4d739 Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 28 Feb 2025 14:11:22 +0000 Subject: [PATCH] Build branch v0.5 with version v0.5.5 (04bc538) Build pipeline: viash-hub.htrnaseq.v0.5-nr288 Source commit: https://github.com/viash-hub/htrnaseq/commit/04bc53879dc3f81f5792359eab8fa6dbf697ac4f Source message: Bump version to v0.5.5 --- CHANGELOG.md | 6 +++++ _viash.yaml | 2 +- src/workflows/runner/config.vsh.yaml | 6 +++++ src/workflows/runner/main.nf | 1 + .../eset/create_eset/.config.vsh.yaml | 11 ++++---- .../executable/eset/create_eset/create_eset | 14 +++++----- .../eset/create_fdata/.config.vsh.yaml | 11 ++++---- .../executable/eset/create_fdata/create_fdata | 14 +++++----- .../eset/create_pdata/.config.vsh.yaml | 11 ++++---- .../executable/eset/create_pdata/create_pdata | 14 +++++----- .../htrnaseq/check_eset/.config.vsh.yaml | 11 ++++---- .../htrnaseq/check_eset/check_eset | 14 +++++----- .../check_cutadapt_output/.config.vsh.yaml | 11 ++++---- .../check_cutadapt_output | 14 +++++----- .../io/publish_fastqs/.config.vsh.yaml | 11 ++++---- .../io/publish_fastqs/publish_fastqs | 14 +++++----- .../io/publish_results/.config.vsh.yaml | 11 ++++---- .../io/publish_results/publish_results | 14 +++++----- .../executable/parallel_map/.config.vsh.yaml | 11 ++++---- target/executable/parallel_map/parallel_map | 14 +++++----- .../report/create_report/.config.vsh.yaml | 11 ++++---- .../report/create_report/create_report | 14 +++++----- .../stats/combine_star_logs/.config.vsh.yaml | 11 ++++---- .../stats/combine_star_logs/combine_star_logs | 14 +++++----- .../generate_pool_statistics/.config.vsh.yaml | 11 ++++---- .../generate_pool_statistics | 14 +++++----- .../generate_well_statistics/.config.vsh.yaml | 11 ++++---- .../generate_well_statistics | 14 +++++----- .../eset/create_eset/.config.vsh.yaml | 11 ++++---- target/nextflow/eset/create_eset/main.nf | 17 ++++++------ .../nextflow/eset/create_eset/nextflow.config | 2 +- .../eset/create_fdata/.config.vsh.yaml | 11 ++++---- target/nextflow/eset/create_fdata/main.nf | 17 ++++++------ .../eset/create_fdata/nextflow.config | 2 +- .../eset/create_pdata/.config.vsh.yaml | 11 ++++---- target/nextflow/eset/create_pdata/main.nf | 17 ++++++------ .../eset/create_pdata/nextflow.config | 2 +- .../htrnaseq/check_eset/.config.vsh.yaml | 11 ++++---- .../htrnaseq/check_eset/main.nf | 17 ++++++------ .../htrnaseq/check_eset/nextflow.config | 2 +- .../check_cutadapt_output/.config.vsh.yaml | 11 ++++---- .../check_cutadapt_output/main.nf | 17 ++++++------ .../check_cutadapt_output/nextflow.config | 2 +- .../io/publish_fastqs/.config.vsh.yaml | 11 ++++---- target/nextflow/io/publish_fastqs/main.nf | 17 ++++++------ .../io/publish_fastqs/nextflow.config | 2 +- .../io/publish_results/.config.vsh.yaml | 11 ++++---- target/nextflow/io/publish_results/main.nf | 17 ++++++------ .../io/publish_results/nextflow.config | 2 +- target/nextflow/parallel_map/.config.vsh.yaml | 11 ++++---- target/nextflow/parallel_map/main.nf | 17 ++++++------ target/nextflow/parallel_map/nextflow.config | 2 +- .../report/create_report/.config.vsh.yaml | 11 ++++---- target/nextflow/report/create_report/main.nf | 17 ++++++------ .../report/create_report/nextflow.config | 2 +- .../stats/combine_star_logs/.config.vsh.yaml | 11 ++++---- .../nextflow/stats/combine_star_logs/main.nf | 17 ++++++------ .../stats/combine_star_logs/nextflow.config | 2 +- .../generate_pool_statistics/.config.vsh.yaml | 11 ++++---- .../stats/generate_pool_statistics/main.nf | 17 ++++++------ .../generate_pool_statistics/nextflow.config | 2 +- .../generate_well_statistics/.config.vsh.yaml | 11 ++++---- .../stats/generate_well_statistics/main.nf | 17 ++++++------ .../generate_well_statistics/nextflow.config | 2 +- .../utils/listInputDir/.config.vsh.yaml | 9 ++++--- target/nextflow/utils/listInputDir/main.nf | 13 ++++----- .../utils/listInputDir/nextflow.config | 2 +- .../workflows/htrnaseq/.config.vsh.yaml | 9 ++++--- target/nextflow/workflows/htrnaseq/main.nf | 13 ++++----- .../workflows/htrnaseq/nextflow.config | 2 +- .../workflows/runner/.config.vsh.yaml | 20 +++++++++++--- target/nextflow/workflows/runner/main.nf | 27 ++++++++++++++----- .../nextflow/workflows/runner/nextflow.config | 2 +- .../workflows/runner/nextflow_schema.json | 11 ++++++++ .../well_demultiplex/.config.vsh.yaml | 9 ++++--- .../workflows/well_demultiplex/main.nf | 13 ++++----- .../well_demultiplex/nextflow.config | 2 +- .../workflows/well_metadata/.config.vsh.yaml | 9 ++++--- .../nextflow/workflows/well_metadata/main.nf | 13 ++++----- .../workflows/well_metadata/nextflow.config | 2 +- 80 files changed, 463 insertions(+), 368 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 03041c1c..ffb3124a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# htrnaseq v0.5.5 + +## New functionality + +* Add `umi_length` parameter to the `runner` workflow (PR #46) + # htrnaseq v0.5.4 * Fix missing barcodes in the output from `generate_pool_statistics`, which caused an assertion error in `create_pdata`. diff --git a/_viash.yaml b/_viash.yaml index f7c3092a..c50948fd 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.5.4 +version: v0.5.5 description: | High-throughput pipeline [WIP] license: MIT diff --git a/src/workflows/runner/config.vsh.yaml b/src/workflows/runner/config.vsh.yaml index 6bdd5a05..0b11ea2d 100644 --- a/src/workflows/runner/config.vsh.yaml +++ b/src/workflows/runner/config.vsh.yaml @@ -23,6 +23,12 @@ argument_groups: type: string multiple: true default: ["Undetermined"] + - name: "--umi_length" + description: | + Length of the UMI sequences + type: integer + min: 1 + default: 10 - name: Metadata arguments arguments: - name: --id diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index 27764447..6864ddd7 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -75,6 +75,7 @@ workflow run_wf { barcodesFasta: "barcodesFasta", genomeDir: "genomeDir", annotation: "annotation", + umi_length: "umi_length", ], toState: { id, result, state -> state + result } ) diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index b06f13b8..4aad4d70 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_eset" namespace: "eset" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -172,7 +172,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "r" @@ -198,11 +198,12 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +218,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index f97d8eef..c91c953f 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_eset v0.5.4 +# create_eset v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_eset v0.5.4" + echo "create_eset v0.5.5" echo "" echo "Arguments:" echo " --pDataFile" @@ -477,10 +477,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_eset" -LABEL org.opencontainers.image.created="2025-02-21T11:04:39Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -616,7 +616,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_eset v0.5.4" + echo "create_eset v0.5.5" exit ;; --pDataFile) @@ -768,7 +768,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.5.5' fi # print dockerfile diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index bae88042..67005179 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_fdata" namespace: "eset" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -148,7 +148,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -177,11 +177,12 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -196,7 +197,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index c115b855..b152426f 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_fdata v0.5.4 +# create_fdata v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_fdata v0.5.4" + echo "create_fdata v0.5.5" echo "" echo "Create a fdata file" echo "" @@ -478,10 +478,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-02-21T11:04:40Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:35Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -617,7 +617,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_fdata v0.5.4" + echo "create_fdata v0.5.5" exit ;; --gtf) @@ -730,7 +730,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.5.5' fi # print dockerfile diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 0c5c3963..fbb81803 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pdata" namespace: "eset" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -191,11 +191,12 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -210,7 +211,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index eb001405..a4e141f1 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_pdata v0.5.4 +# create_pdata v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pdata v0.5.4" + echo "create_pdata v0.5.5" echo "" echo "Create a pdata file by combining the mapping statistics" echo "" @@ -488,10 +488,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-02-21T11:04:39Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:37Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -627,7 +627,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pdata v0.5.4" + echo "create_pdata v0.5.5" exit ;; --star_stats_file) @@ -751,7 +751,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.5.5' 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 dc695aea..45bff430 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_eset" namespace: "integration_test_components/htrnaseq" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "r" @@ -148,11 +148,12 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -167,7 +168,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index 68ec1ace..ff9f22bd 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# check_eset v0.5.4 +# check_eset v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_eset v0.5.4" + echo "check_eset v0.5.5" echo "" echo "This component test the ExpressionSet object as output by the main pipeline." echo "" @@ -470,10 +470,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset" -LABEL org.opencontainers.image.created="2025-02-21T11:04:40Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:37Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_eset v0.5.4" + echo "check_eset v0.5.5" exit ;; --eset) @@ -728,7 +728,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.5.5' 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 28129731..ec7e6859 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_cutadapt_output" namespace: "integration_test_components/well_demultiplexing" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -135,7 +135,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -158,11 +158,12 @@ build_info: output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -177,7 +178,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output index 274fa724..ddb71479 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# check_cutadapt_output v0.5.4 +# check_cutadapt_output v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_cutadapt_output v0.5.4" + echo "check_cutadapt_output v0.5.5" echo "" echo "This component test the cutadapt output from the well_demultiplex subworkflow." echo "" @@ -476,10 +476,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-02-21T11:04:39Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_cutadapt_output v0.5.4" + echo "check_cutadapt_output v0.5.5" exit ;; --fastq_r1) @@ -757,7 +757,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.5.5' fi # print dockerfile diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 0a219d19..5bbca8ad 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_fastqs" namespace: "io" -version: "v0.5.4" +version: "v0.5.5" argument_groups: - name: "Input arguments" arguments: @@ -125,7 +125,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -143,11 +143,12 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -162,7 +163,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index e7ae76e8..6e4b1801 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish_fastqs v0.5.4 +# publish_fastqs v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_fastqs v0.5.4" + echo "publish_fastqs v0.5.5" echo "" echo "Publish the fastq files per well" echo "" @@ -470,10 +470,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-02-21T11:04:38Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_fastqs v0.5.4" + echo "publish_fastqs v0.5.5" exit ;; --input_r1) @@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.5.5' fi # print dockerfile diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index ce3d32e7..2fff4a0e 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_results" namespace: "io" -version: "v0.5.4" +version: "v0.5.5" argument_groups: - name: "Input arguments" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -187,11 +187,12 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -206,7 +207,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index dcca4ae6..730973c8 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish_results v0.5.4 +# publish_results v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_results v0.5.4" + echo "publish_results v0.5.5" echo "" echo "Publish the results" echo "" @@ -484,10 +484,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-02-21T11:04:38Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:35Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -623,7 +623,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_results v0.5.4" + echo "publish_results v0.5.5" exit ;; --star_output) @@ -838,7 +838,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.5.5' fi # print dockerfile diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 1ca29a5b..d88b362b 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "parallel_map" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -242,7 +242,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,12 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -298,7 +299,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index ef6a257e..7ea55343 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# parallel_map v0.5.4 +# parallel_map v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "parallel_map v0.5.4" + echo "parallel_map v0.5.5" echo "" echo "Map wells in batch, using STAR" echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin" @@ -540,10 +540,10 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-02-21T11:04:40Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:37Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -679,7 +679,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "parallel_map v0.5.4" + echo "parallel_map v0.5.5" exit ;; --input_r1) @@ -881,7 +881,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.5.5' fi # print dockerfile diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index be0f0e6e..88db9e22 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_report" namespace: "report" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -201,11 +201,12 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -220,7 +221,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 21da6689..91c9b516 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_report v0.5.4 +# create_report v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_report v0.5.4" + echo "create_report v0.5.5" echo "" echo "Create a basic QC report in HTML format based on a number of esets." echo "" @@ -476,10 +476,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component report create_report" -LABEL org.opencontainers.image.created="2025-02-21T11:04:40Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_report v0.5.4" + echo "create_report v0.5.5" exit ;; --eset) @@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.5.5' 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 2768473d..9f6c3874 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_star_logs" namespace: "stats" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -169,7 +169,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,12 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +218,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index c008d7dd..c7c64627 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# combine_star_logs v0.5.4 +# combine_star_logs v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -174,7 +174,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "combine_star_logs v0.5.4" + echo "combine_star_logs v0.5.5" echo "" echo "Arguments:" echo " --barcodes" @@ -490,10 +490,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-02-21T11:04:38Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:37Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "combine_star_logs v0.5.4" + echo "combine_star_logs v0.5.5" exit ;; --barcodes) @@ -799,7 +799,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.5.5' 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 8dca334e..98bef0d3 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_pool_statistics" namespace: "stats" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -182,11 +182,12 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -201,7 +202,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 7d04617e..92bf9fed 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# generate_pool_statistics v0.5.4 +# generate_pool_statistics v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_pool_statistics v0.5.4" + echo "generate_pool_statistics v0.5.5" echo "" echo "Arguments:" echo " --nrReadsNrGenesPerChrom" @@ -483,10 +483,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-02-21T11:04:38Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_pool_statistics v0.5.4" + echo "generate_pool_statistics v0.5.5" exit ;; --nrReadsNrGenesPerChrom) @@ -741,7 +741,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.5.5' 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 e03a72b9..cbd8edd1 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_well_statistics" namespace: "stats" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,12 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -283,7 +284,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index e7beb626..94c9840e 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# generate_well_statistics v0.5.4 +# generate_well_statistics v0.5.5 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -175,7 +175,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_well_statistics v0.5.4" + echo "generate_well_statistics v0.5.5" echo "" echo "Generate summary statistics from BAM files generated by STAR solo." echo "" @@ -520,10 +520,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-02-21T11:04:39Z" +LABEL org.opencontainers.image.created="2025-02-28T13:28:36Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="e41d8828866c686d58001cec72ff3e86b2ddf9dc" -LABEL org.opencontainers.image.version="v0.5.4" +LABEL org.opencontainers.image.revision="04bc53879dc3f81f5792359eab8fa6dbf697ac4f" +LABEL org.opencontainers.image.version="v0.5.5" VIASHDOCKER fi @@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_well_statistics v0.5.4" + echo "generate_well_statistics v0.5.5" exit ;; --input) @@ -838,7 +838,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.5.4' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.5.5' fi # print dockerfile diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 21bddb8e..72b9fe37 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_eset" namespace: "eset" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -172,7 +172,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "r" @@ -198,11 +198,12 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +218,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index a7784cb1..1694dee1 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -1,4 +1,4 @@ -// create_eset v0.5.4 +// create_eset v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_eset", "namespace" : "eset", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3036,7 +3036,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3072,12 +3072,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3094,7 +3095,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3946,7 +3947,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_eset", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_eset/nextflow.config b/target/nextflow/eset/create_eset/nextflow.config index 20186a3c..75f9aa5c 100644 --- a/target/nextflow/eset/create_eset/nextflow.config +++ b/target/nextflow/eset/create_eset/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_eset' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 640539df..124cd06c 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_fdata" namespace: "eset" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -148,7 +148,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -177,11 +177,12 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -196,7 +197,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index 829b09ce..ee715f5f 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -1,4 +1,4 @@ -// create_fdata v0.5.4 +// create_fdata v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_fdata", "namespace" : "eset", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3003,7 +3003,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3044,12 +3044,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3066,7 +3067,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3613,7 +3614,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_fdata", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_fdata/nextflow.config b/target/nextflow/eset/create_fdata/nextflow.config index 427a85b7..c972eb0a 100644 --- a/target/nextflow/eset/create_fdata/nextflow.config +++ b/target/nextflow/eset/create_fdata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_fdata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 04f2390c..0ae418fb 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pdata" namespace: "eset" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -162,7 +162,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -191,11 +191,12 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -210,7 +211,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index 8ccfa696..14807424 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -1,4 +1,4 @@ -// create_pdata v0.5.4 +// create_pdata v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_pdata", "namespace" : "eset", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3017,7 +3017,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3058,12 +3058,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3080,7 +3081,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3553,7 +3554,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_pdata", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_pdata/nextflow.config b/target/nextflow/eset/create_pdata/nextflow.config index a368a688..0c85d3f7 100644 --- a/target/nextflow/eset/create_pdata/nextflow.config +++ b/target/nextflow/eset/create_pdata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_pdata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 a0bf0ff6..1aa39483 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_eset" namespace: "integration_test_components/htrnaseq" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -128,7 +128,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "r" @@ -148,11 +148,12 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -167,7 +168,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index 2b4f0f80..78647a29 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -1,4 +1,4 @@ -// check_eset v0.5.4 +// check_eset v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_eset", "namespace" : "integration_test_components/htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -2971,7 +2971,7 @@ meta = [ "id" : "docker", "image" : "bioconductor/bioconductor_docker:3.19", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -2997,12 +2997,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3019,7 +3020,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3646,7 +3647,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "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 b1a08eb9..01f624ea 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integration_test_components/htrnaseq/check_eset' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 1d68d9a2..9b56ecf8 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_cutadapt_output" namespace: "integration_test_components/well_demultiplexing" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -135,7 +135,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -158,11 +158,12 @@ build_info: output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -177,7 +178,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf index 0ee5e348..3deb39c5 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -1,4 +1,4 @@ -// check_cutadapt_output v0.5.4 +// check_cutadapt_output v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_cutadapt_output", "namespace" : "integration_test_components/well_demultiplexing", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -2978,7 +2978,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3009,12 +3009,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3031,7 +3032,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3527,7 +3528,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "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 bd44cdab..c4adc066 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integration_test_components/well_demultiplexing/check_cutadapt_output' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 e94dcbba..76c37650 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_fastqs" namespace: "io" -version: "v0.5.4" +version: "v0.5.5" argument_groups: - name: "Input arguments" arguments: @@ -125,7 +125,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -143,11 +143,12 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -162,7 +163,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 03f92d89..f87e57ac 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -1,4 +1,4 @@ -// publish_fastqs v0.5.4 +// publish_fastqs v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish_fastqs", "namespace" : "io", - "version" : "v0.5.4", + "version" : "v0.5.5", "argument_groups" : [ { "name" : "Input arguments", @@ -2960,7 +2960,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -2983,12 +2983,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3005,7 +3006,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3440,7 +3441,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_fastqs", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_fastqs/nextflow.config b/target/nextflow/io/publish_fastqs/nextflow.config index 9d74a128..4eff0cf2 100644 --- a/target/nextflow/io/publish_fastqs/nextflow.config +++ b/target/nextflow/io/publish_fastqs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_fastqs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 d2428bdb..1822b259 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_results" namespace: "io" -version: "v0.5.4" +version: "v0.5.5" argument_groups: - name: "Input arguments" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -187,11 +187,12 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -206,7 +207,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index 713c20b6..234ceca8 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -1,4 +1,4 @@ -// publish_results v0.5.4 +// publish_results v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish_results", "namespace" : "io", - "version" : "v0.5.4", + "version" : "v0.5.5", "argument_groups" : [ { "name" : "Input arguments", @@ -3009,7 +3009,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3032,12 +3032,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3054,7 +3055,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3516,7 +3517,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_results", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_results/nextflow.config b/target/nextflow/io/publish_results/nextflow.config index c4b03877..c3b954c4 100644 --- a/target/nextflow/io/publish_results/nextflow.config +++ b/target/nextflow/io/publish_results/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_results' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' description = 'Publish the results' } diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 812f0e06..f25c88e1 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "parallel_map" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -242,7 +242,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,12 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -298,7 +299,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index f3e8f089..a395dca9 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -1,4 +1,4 @@ -// parallel_map v0.5.4 +// parallel_map v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "parallel_map", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3097,7 +3097,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3144,12 +3144,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3166,7 +3167,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3911,7 +3912,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/parallel_map", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/parallel_map/nextflow.config b/target/nextflow/parallel_map/nextflow.config index 1658c6cd..d8e56c1c 100644 --- a/target/nextflow/parallel_map/nextflow.config +++ b/target/nextflow/parallel_map/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'parallel_map' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 9a84c12e..72aae1f8 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_report" namespace: "report" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -201,11 +201,12 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -220,7 +221,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index 13da11ea..7c210962 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -1,4 +1,4 @@ -// create_report v0.5.4 +// create_report v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_report", "namespace" : "report", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3016,7 +3016,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3077,12 +3077,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3099,7 +3100,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3561,7 +3562,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/report/create_report", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/create_report/nextflow.config b/target/nextflow/report/create_report/nextflow.config index 7cb5c474..e6b41a8b 100644 --- a/target/nextflow/report/create_report/nextflow.config +++ b/target/nextflow/report/create_report/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'report/create_report' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 17236789..d880eb24 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_star_logs" namespace: "stats" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -169,7 +169,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -198,11 +198,12 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -217,7 +218,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index b9a57467..f2b5fac4 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -1,4 +1,4 @@ -// combine_star_logs v0.5.4 +// combine_star_logs v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_star_logs", "namespace" : "stats", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3019,7 +3019,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3060,12 +3060,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3082,7 +3083,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3718,7 +3719,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/combine_star_logs", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/combine_star_logs/nextflow.config b/target/nextflow/stats/combine_star_logs/nextflow.config index 79ffe59f..fc1034bf 100644 --- a/target/nextflow/stats/combine_star_logs/nextflow.config +++ b/target/nextflow/stats/combine_star_logs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/combine_star_logs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 6f7d833f..28ff036b 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_pool_statistics" namespace: "stats" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -153,7 +153,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "apt" @@ -182,11 +182,12 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -201,7 +202,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 8654e929..dfda4dc1 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -1,4 +1,4 @@ -// generate_pool_statistics v0.5.4 +// generate_pool_statistics v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_pool_statistics", "namespace" : "stats", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3003,7 +3003,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3044,12 +3044,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3066,7 +3067,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3573,7 +3574,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_pool_statistics", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_pool_statistics/nextflow.config b/target/nextflow/stats/generate_pool_statistics/nextflow.config index cd0658cc..aaec79fb 100644 --- a/target/nextflow/stats/generate_pool_statistics/nextflow.config +++ b/target/nextflow/stats/generate_pool_statistics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/generate_pool_statistics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 334ccd75..4163ed98 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_well_statistics" namespace: "stats" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -224,7 +224,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.5.4" + target_tag: "v0.5.5" namespace_separator: "/" setup: - type: "docker" @@ -264,11 +264,12 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -283,7 +284,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index 427ec839..6d99d5be 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -1,4 +1,4 @@ -// generate_well_statistics v0.5.4 +// generate_well_statistics v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_well_statistics", "namespace" : "stats", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3084,7 +3084,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.5.4", + "target_tag" : "v0.5.5", "namespace_separator" : "/", "setup" : [ { @@ -3139,12 +3139,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3161,7 +3162,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3659,7 +3660,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_well_statistics", - "tag" : "v0.5.4" + "tag" : "v0.5.5" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_well_statistics/nextflow.config b/target/nextflow/stats/generate_well_statistics/nextflow.config index e10e818d..ac294b9f 100644 --- a/target/nextflow/stats/generate_well_statistics/nextflow.config +++ b/target/nextflow/stats/generate_well_statistics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/generate_well_statistics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' description = 'Generate summary statistics from BAM files generated by STAR solo.' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index 887ad8ce..14cc1cd6 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "listInputDir" namespace: "utils" -version: "v0.5.4" +version: "v0.5.5" argument_groups: - name: "Arguments" arguments: @@ -165,11 +165,12 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -184,7 +185,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index d21e488d..4eaeb085 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -1,4 +1,4 @@ -// listInputDir v0.5.4 +// listInputDir v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "listInputDir", "namespace" : "utils", - "version" : "v0.5.4", + "version" : "v0.5.5", "argument_groups" : [ { "name" : "Arguments", @@ -3004,12 +3004,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3026,7 +3027,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/utils/listInputDir/nextflow.config b/target/nextflow/utils/listInputDir/nextflow.config index 1c236487..791386f9 100644 --- a/target/nextflow/utils/listInputDir/nextflow.config +++ b/target/nextflow/utils/listInputDir/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/listInputDir' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' description = 'List the contents of a directory and parse contained fastq files' } diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index 1c26dc3e..db796876 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htrnaseq" namespace: "workflows" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -323,8 +323,9 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" dependencies: - "target/nextflow/stats/combine_star_logs" - "target/nextflow/stats/generate_pool_statistics" @@ -338,7 +339,7 @@ build_info: - "target/nextflow/report/create_report" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -353,7 +354,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index 45295888..d44c9cc3 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -1,4 +1,4 @@ -// htrnaseq v0.5.4 +// htrnaseq v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "htrnaseq", "namespace" : "workflows", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3229,12 +3229,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3251,7 +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", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/htrnaseq/nextflow.config b/target/nextflow/workflows/htrnaseq/nextflow.config index 4b9995d6..f557d848 100644 --- a/target/nextflow/workflows/htrnaseq/nextflow.config +++ b/target/nextflow/workflows/htrnaseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/htrnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index 667ab867..500e7dc6 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "runner" namespace: "workflows" -version: "v0.5.4" +version: "v0.5.5" argument_groups: - name: "Input arguments" arguments: @@ -51,6 +51,17 @@ argument_groups: direction: "input" multiple: true multiple_sep: ";" + - type: "integer" + name: "--umi_length" + description: "Length of the UMI sequences\n" + info: null + default: + - 10 + required: false + min: 1 + direction: "input" + multiple: false + multiple_sep: ";" - name: "Metadata arguments" arguments: - type: "string" @@ -207,8 +218,9 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" dependencies: - "target/nextflow/utils/listInputDir" - "target/nextflow/workflows/htrnaseq" @@ -216,7 +228,7 @@ build_info: - "target/nextflow/io/publish_results" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -231,7 +243,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index f2362de1..5d24064f 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.5.4 +// runner v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "runner", "namespace" : "workflows", - "version" : "v0.5.4", + "version" : "v0.5.5", "argument_groups" : [ { "name" : "Input arguments", @@ -2863,6 +2863,19 @@ meta = [ "direction" : "input", "multiple" : true, "multiple_sep" : ";" + }, + { + "type" : "integer", + "name" : "--umi_length", + "description" : "Length of the UMI sequences\n", + "default" : [ + 10 + ], + "required" : false, + "min" : 1, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3069,12 +3082,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3091,7 +3105,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", @@ -3197,6 +3211,7 @@ workflow run_wf { barcodesFasta: "barcodesFasta", genomeDir: "genomeDir", annotation: "annotation", + umi_length: "umi_length", ], toState: { id, result, state -> state + result } ) diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config index 8ba257e3..6bf28669 100644 --- a/target/nextflow/workflows/runner/nextflow.config +++ b/target/nextflow/workflows/runner/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/runner' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' description = 'Runner for HT RNA-seq pipeline' } diff --git a/target/nextflow/workflows/runner/nextflow_schema.json b/target/nextflow/workflows/runner/nextflow_schema.json index cfa52cfc..e88fb039 100644 --- a/target/nextflow/workflows/runner/nextflow_schema.json +++ b/target/nextflow/workflows/runner/nextflow_schema.json @@ -64,6 +64,17 @@ } + , + "umi_length": { + "type": + "integer", + "description": "Type: `integer`, default: `10`. Length of the UMI sequences\n", + "help_text": "Type: `integer`, default: `10`. Length of the UMI sequences\n" + , + "default":10 + } + + } }, diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 2ff28550..6ebea97e 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_demultiplex" namespace: "workflows" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -211,14 +211,15 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/cutadapt" - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/concat_text" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -233,7 +234,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index a6d4a1b1..5b21100e 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -1,4 +1,4 @@ -// well_demultiplex v0.5.4 +// well_demultiplex v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2810,7 +2810,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_demultiplex", "namespace" : "workflows", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3084,12 +3084,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3106,7 +3107,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_demultiplex/nextflow.config b/target/nextflow/workflows/well_demultiplex/nextflow.config index 9e4a39da..d6bf6d06 100644 --- a/target/nextflow/workflows/well_demultiplex/nextflow.config +++ b/target/nextflow/workflows/well_demultiplex/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_demultiplex' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' 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 651d6c47..d6d8bf4d 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_metadata" namespace: "workflows" -version: "v0.5.4" +version: "v0.5.5" authors: - name: "Dries Schaumont" roles: @@ -209,11 +209,12 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.0" - git_commit: "e41d8828866c686d58001cec72ff3e86b2ddf9dc" + git_commit: "04bc53879dc3f81f5792359eab8fa6dbf697ac4f" git_remote: "https://github.com/viash-hub/htrnaseq" + git_tag: "v0.5.4-3-g04bc538" package_config: name: "htrnaseq" - version: "v0.5.4" + version: "v0.5.5" description: "High-throughput pipeline [WIP]\n" info: test_resources: @@ -228,7 +229,7 @@ package_config: \ dest: 'nextflow_labels.config'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + - ".engines[.type == 'docker'].target_tag := 'v0.5.5'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index 248019d2..c1903ed8 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -1,4 +1,4 @@ -// well_metadata v0.5.4 +// well_metadata v0.5.5 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2809,7 +2809,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_metadata", "namespace" : "workflows", - "version" : "v0.5.4", + "version" : "v0.5.5", "authors" : [ { "name" : "Dries Schaumont", @@ -3064,12 +3064,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.0", - "git_commit" : "e41d8828866c686d58001cec72ff3e86b2ddf9dc", - "git_remote" : "https://github.com/viash-hub/htrnaseq" + "git_commit" : "04bc53879dc3f81f5792359eab8fa6dbf697ac4f", + "git_remote" : "https://github.com/viash-hub/htrnaseq", + "git_tag" : "v0.5.4-3-g04bc538" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.5.4", + "version" : "v0.5.5", "description" : "High-throughput pipeline [WIP]\n", "info" : { "test_resources" : [ @@ -3086,7 +3087,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.5.4'" + ".engines[.type == 'docker'].target_tag := 'v0.5.5'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_metadata/nextflow.config b/target/nextflow/workflows/well_metadata/nextflow.config index 30622853..c5a3aafc 100644 --- a/target/nextflow/workflows/well_metadata/nextflow.config +++ b/target/nextflow/workflows/well_metadata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_metadata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.5.4' + version = 'v0.5.5' author = 'Dries Schaumont' }