From fbbb4d6cfe430fbb76301531ca8a5282ba4a71c5 Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 1 Aug 2025 13:52:19 +0000 Subject: [PATCH] Build branch v0.4 with version v0.4.3 (aa88037) Build pipeline: viash-hub.demultiplex.v0.4-6v7tp Source commit: https://github.com/viash-hub/demultiplex/commit/aa8803720f098287518db3d2dc74eff24cf003f1 Source message: Bump version to v0.4.3 --- CHANGELOG.md | 6 ++++++ _viash.yaml | 2 +- src/runner/main.nf | 9 ++++++++ src/runner/test.nf | 4 ++-- .../interop_summary_to_csv/.config.vsh.yaml | 12 +++++------ .../io/interop_summary_to_csv/_viash.yaml | 2 +- .../interop_summary_to_csv | 14 ++++++------- target/executable/io/publish/.config.vsh.yaml | 12 +++++------ target/executable/io/publish/_viash.yaml | 2 +- target/executable/io/publish/publish | 14 ++++++------- target/executable/io/untar/.config.vsh.yaml | 12 +++++------ target/executable/io/untar/_viash.yaml | 2 +- target/executable/io/untar/untar | 14 ++++++------- .../dataflow/combine_samples/.config.vsh.yaml | 10 ++++----- .../dataflow/combine_samples/_viash.yaml | 2 +- .../nextflow/dataflow/combine_samples/main.nf | 12 +++++------ .../dataflow/combine_samples/nextflow.config | 2 +- .../.config.vsh.yaml | 10 ++++----- .../gather_fastqs_and_validate/_viash.yaml | 2 +- .../gather_fastqs_and_validate/main.nf | 12 +++++------ .../nextflow.config | 2 +- target/nextflow/demultiplex/.config.vsh.yaml | 10 ++++----- target/nextflow/demultiplex/_viash.yaml | 2 +- target/nextflow/demultiplex/main.nf | 12 +++++------ target/nextflow/demultiplex/nextflow.config | 2 +- .../detect_demultiplexer/.config.vsh.yaml | 10 ++++----- .../nextflow/detect_demultiplexer/_viash.yaml | 2 +- target/nextflow/detect_demultiplexer/main.nf | 12 +++++------ .../detect_demultiplexer/nextflow.config | 2 +- .../interop_summary_to_csv/.config.vsh.yaml | 12 +++++------ .../io/interop_summary_to_csv/_viash.yaml | 2 +- .../io/interop_summary_to_csv/main.nf | 16 +++++++------- .../io/interop_summary_to_csv/nextflow.config | 2 +- target/nextflow/io/publish/.config.vsh.yaml | 12 +++++------ target/nextflow/io/publish/_viash.yaml | 2 +- target/nextflow/io/publish/main.nf | 16 +++++++------- target/nextflow/io/publish/nextflow.config | 2 +- target/nextflow/io/untar/.config.vsh.yaml | 12 +++++------ target/nextflow/io/untar/_viash.yaml | 2 +- target/nextflow/io/untar/main.nf | 16 +++++++------- target/nextflow/io/untar/nextflow.config | 2 +- target/nextflow/runner/.config.vsh.yaml | 10 ++++----- target/nextflow/runner/_viash.yaml | 2 +- target/nextflow/runner/main.nf | 21 +++++++++++++------ target/nextflow/runner/nextflow.config | 2 +- 45 files changed, 182 insertions(+), 158 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 957fa6a..37c8da9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# demultiplex v0.4.3 + +## Minor changes + +* The `runner` creates a `transfer_completed.txt` file when the publishing of the output has finished (PR #57). + # demultiplex v0.4.2 ## Minor changes diff --git a/_viash.yaml b/_viash.yaml index 68e3bf9..cef6a4d 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/src/runner/main.nf b/src/runner/main.nf index ed25d2d..78cba99 100644 --- a/src/runner/main.nf +++ b/src/runner/main.nf @@ -68,6 +68,15 @@ workflow run_wf { println("Publising to ${params.publish_dir}/${prefix}") + // Create a file to indicate that the publishing (transfer) of files has been completed. + // Multiple items can be added to onCompleteActions; which is required when processing multiple sequencing runs at a time. + // Alternatively setOnComplete could be used to add actions, but that only adds them at the end of the list (which is executed in order). + // The 'completed.txt' file must be created before the onComplete of the integration tests are run, so we need to prepend to the list. + workflow.onCompleteActions.add(0, { + def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt") + complete_file.text = "" // This will create a file when it does not exist. + }) + [ input: state.output, input_sample_qc: state.output_sample_qc, diff --git a/src/runner/test.nf b/src/runner/test.nf index afccaed..54832db 100644 --- a/src/runner/test.nf +++ b/src/runner/test.nf @@ -56,8 +56,8 @@ workflow test { // Disabling this test temporarily and creating an issue for it // assert publish_dir.name.endsWith("_demultiplex_unknown_version") def published_items = publish_dir.listFiles() - assert published_items.size() == 4 - assert published_items.collect{it.name}.toSet() == ["demultiplexer_logs", "fastq", "qc", "SampleSheet.csv"].toSet() + assert published_items.size() == 5 + assert published_items.collect{it.name}.toSet() == ["demultiplexer_logs", "fastq", "qc", "SampleSheet.csv", "transfer_completed.txt"].toSet() def fastqc_files = publish_dir.resolve("qc/fastqc").listFiles() assert fastqc_files.collect{it.name}.toSet() == [ "Sample1_S1_L001_R1_001_fastqc_data.txt", diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml index 62250a1..7c895a0 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.2" + target_tag: "v0.4.3" namespace_separator: "/" setup: - type: "apt" @@ -160,12 +160,12 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -181,7 +181,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/interop_summary_to_csv/_viash.yaml b/target/executable/io/interop_summary_to_csv/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/executable/io/interop_summary_to_csv/_viash.yaml +++ b/target/executable/io/interop_summary_to_csv/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv index 349cf22..38a2f78 100755 --- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv +++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# interop_summary_to_csv v0.4.2 +# interop_summary_to_csv v0.4.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -454,10 +454,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \ mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv" -LABEL org.opencontainers.image.created="2025-07-28T12:45:25Z" +LABEL org.opencontainers.image.created="2025-08-01T13:26:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="21de648b218d114d3ab155462f4f08f4d585f741" -LABEL org.opencontainers.image.version="v0.4.2" +LABEL org.opencontainers.image.revision="aa8803720f098287518db3d2dc74eff24cf003f1" +LABEL org.opencontainers.image.version="v0.4.3" VIASHDOCKER fi @@ -574,7 +574,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "interop_summary_to_csv v0.4.2" + echo "interop_summary_to_csv v0.4.3" echo "" echo "Input arguments:" echo " --input" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "interop_summary_to_csv v0.4.2" + echo "interop_summary_to_csv v0.4.3" exit ;; --input) @@ -759,7 +759,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.4.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.4.3' fi # print dockerfile diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index a0dd63c..1ea90f8 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -204,7 +204,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.2" + target_tag: "v0.4.3" namespace_separator: "/" setup: - type: "apt" @@ -222,12 +222,12 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -243,7 +243,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish/_viash.yaml b/target/executable/io/publish/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/executable/io/publish/_viash.yaml +++ b/target/executable/io/publish/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 5b2bbcb..5ec5d61 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish v0.4.2 +# publish v0.4.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish" -LABEL org.opencontainers.image.created="2025-07-28T12:45:25Z" +LABEL org.opencontainers.image.created="2025-08-01T13:26:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="21de648b218d114d3ab155462f4f08f4d585f741" -LABEL org.opencontainers.image.version="v0.4.2" +LABEL org.opencontainers.image.revision="aa8803720f098287518db3d2dc74eff24cf003f1" +LABEL org.opencontainers.image.version="v0.4.3" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish v0.4.2" + echo "publish v0.4.3" echo "" echo "Publish the processed results of the run" echo "" @@ -662,7 +662,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish v0.4.2" + echo "publish v0.4.3" exit ;; --input) @@ -869,7 +869,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.4.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.4.3' fi # print dockerfile diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 3d809a8..69e8030 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.2" + target_tag: "v0.4.3" namespace_separator: "/" setup: - type: "apt" @@ -159,12 +159,12 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -180,7 +180,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/untar/_viash.yaml b/target/executable/io/untar/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/executable/io/untar/_viash.yaml +++ b/target/executable/io/untar/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 8bc9af0..92d43a5 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# untar v0.4.2 +# untar v0.4.3 # # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -450,10 +450,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io untar" -LABEL org.opencontainers.image.created="2025-07-28T12:45:25Z" +LABEL org.opencontainers.image.created="2025-08-01T13:26:46Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="21de648b218d114d3ab155462f4f08f4d585f741" -LABEL org.opencontainers.image.version="v0.4.2" +LABEL org.opencontainers.image.revision="aa8803720f098287518db3d2dc74eff24cf003f1" +LABEL org.opencontainers.image.version="v0.4.3" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "untar v0.4.2" + echo "untar v0.4.3" echo "" echo "Unpack a .tar file. When the contents of the .tar file is just a single" echo "directory," @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "untar v0.4.2" + echo "untar v0.4.3" exit ;; --input) @@ -771,7 +771,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.4.2' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.4.3' fi # print dockerfile diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index 2b71f27..c35a48a 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_samples" namespace: "dataflow" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -168,12 +168,12 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -189,7 +189,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/combine_samples/_viash.yaml b/target/nextflow/dataflow/combine_samples/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/dataflow/combine_samples/_viash.yaml +++ b/target/nextflow/dataflow/combine_samples/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index d704764..e351204 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -1,4 +1,4 @@ -// combine_samples v0.4.2 +// combine_samples v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_samples", "namespace" : "dataflow", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3235,13 +3235,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3258,7 +3258,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config index bd283b0..65f4256 100644 --- a/target/nextflow/dataflow/combine_samples/nextflow.config +++ b/target/nextflow/dataflow/combine_samples/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/combine_samples' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.' } diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml index 4ccbde4..4c33d45 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "gather_fastqs_and_validate" namespace: "dataflow" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -159,12 +159,12 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -180,7 +180,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index ece83c5..fd91d4c 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -1,4 +1,4 @@ -// gather_fastqs_and_validate v0.4.2 +// gather_fastqs_and_validate v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "gather_fastqs_and_validate", "namespace" : "dataflow", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3232,13 +3232,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3255,7 +3255,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config index 1d5a4ad..e8fe435 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/gather_fastqs_and_validate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n' } diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 2c5e86b..b2fbff1 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "demultiplex" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -268,9 +268,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" @@ -283,7 +283,7 @@ build_info: - "target/nextflow/detect_demultiplexer" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -299,7 +299,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/demultiplex/_viash.yaml b/target/nextflow/demultiplex/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/demultiplex/_viash.yaml +++ b/target/nextflow/demultiplex/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index e33869e..163ea3a 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -1,4 +1,4 @@ -// demultiplex v0.4.2 +// demultiplex v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3380,13 +3380,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3403,7 +3403,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config index d61d95a..0a811a3 100644 --- a/target/nextflow/demultiplex/nextflow.config +++ b/target/nextflow/demultiplex/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demultiplex' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'Demultiplexing of raw sequencing data' } diff --git a/target/nextflow/detect_demultiplexer/.config.vsh.yaml b/target/nextflow/detect_demultiplexer/.config.vsh.yaml index 32ac8ab..37a433c 100644 --- a/target/nextflow/detect_demultiplexer/.config.vsh.yaml +++ b/target/nextflow/detect_demultiplexer/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "detect_demultiplexer" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Arguments" arguments: @@ -168,12 +168,12 @@ build_info: output: "target/nextflow/detect_demultiplexer" executable: "target/nextflow/detect_demultiplexer/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -189,7 +189,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/detect_demultiplexer/_viash.yaml b/target/nextflow/detect_demultiplexer/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/detect_demultiplexer/_viash.yaml +++ b/target/nextflow/detect_demultiplexer/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/detect_demultiplexer/main.nf b/target/nextflow/detect_demultiplexer/main.nf index bee244e..aeea363 100644 --- a/target/nextflow/detect_demultiplexer/main.nf +++ b/target/nextflow/detect_demultiplexer/main.nf @@ -1,4 +1,4 @@ -// detect_demultiplexer v0.4.2 +// detect_demultiplexer v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "detect_demultiplexer", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Arguments", @@ -3224,13 +3224,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/detect_demultiplexer", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3247,7 +3247,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/detect_demultiplexer/nextflow.config b/target/nextflow/detect_demultiplexer/nextflow.config index 8be1589..18b4d3c 100644 --- a/target/nextflow/detect_demultiplexer/nextflow.config +++ b/target/nextflow/detect_demultiplexer/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'detect_demultiplexer' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'Detects the demultiplexer and accompanying sample information file which can be \nused to generate the fastq files.\n' } diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml index ebbf7f8..024c955 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.2" + target_tag: "v0.4.3" namespace_separator: "/" setup: - type: "apt" @@ -160,12 +160,12 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -181,7 +181,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/interop_summary_to_csv/_viash.yaml b/target/nextflow/io/interop_summary_to_csv/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/io/interop_summary_to_csv/_viash.yaml +++ b/target/nextflow/io/interop_summary_to_csv/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index 6a71a97..3f23621 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -1,4 +1,4 @@ -// interop_summary_to_csv v0.4.2 +// interop_summary_to_csv v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "interop_summary_to_csv", "namespace" : "io", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3203,7 +3203,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.2", + "target_tag" : "v0.4.3", "namespace_separator" : "/", "setup" : [ { @@ -3233,13 +3233,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3256,7 +3256,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", @@ -3700,7 +3700,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/interop_summary_to_csv", - "tag" : "v0.4.2" + "tag" : "v0.4.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config index 256b5a8..3fc1019 100644 --- a/target/nextflow/io/interop_summary_to_csv/nextflow.config +++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/interop_summary_to_csv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 06bdded..0f2a712 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -204,7 +204,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.2" + target_tag: "v0.4.3" namespace_separator: "/" setup: - type: "apt" @@ -222,12 +222,12 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -243,7 +243,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish/_viash.yaml b/target/nextflow/io/publish/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/io/publish/_viash.yaml +++ b/target/nextflow/io/publish/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 060318f..ce1dda9 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -1,4 +1,4 @@ -// publish v0.4.2 +// publish v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish", "namespace" : "io", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3279,7 +3279,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.2", + "target_tag" : "v0.4.3", "namespace_separator" : "/", "setup" : [ { @@ -3302,13 +3302,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3325,7 +3325,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", @@ -3800,7 +3800,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/publish", - "tag" : "v0.4.2" + "tag" : "v0.4.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config index dbe8038..045ad1f 100644 --- a/target/nextflow/io/publish/nextflow.config +++ b/target/nextflow/io/publish/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'Publish the processed results of the run' } diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 6098c66..0cbd6bd 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.4.2" + target_tag: "v0.4.3" namespace_separator: "/" setup: - type: "apt" @@ -159,12 +159,12 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -180,7 +180,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/untar/_viash.yaml b/target/nextflow/io/untar/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/io/untar/_viash.yaml +++ b/target/nextflow/io/untar/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 1f50b00..e7aeff2 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -1,4 +1,4 @@ -// untar v0.4.2 +// untar v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3032,7 +3032,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "untar", "namespace" : "io", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3209,7 +3209,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.4.2", + "target_tag" : "v0.4.3", "namespace_separator" : "/", "setup" : [ { @@ -3232,13 +3232,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3255,7 +3255,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", @@ -3729,7 +3729,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/untar", - "tag" : "v0.4.2" + "tag" : "v0.4.3" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config index bf0f578..618f0ce 100644 --- a/target/nextflow/io/untar/nextflow.config +++ b/target/nextflow/io/untar/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/untar' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n' } diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 8411cbf..4ff2a70 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "runner" -version: "v0.4.2" +version: "v0.4.3" argument_groups: - name: "Input arguments" arguments: @@ -214,15 +214,15 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.4" - git_commit: "21de648b218d114d3ab155462f4f08f4d585f741" + git_commit: "aa8803720f098287518db3d2dc74eff24cf003f1" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.1.1-40-g21de648" + git_tag: "v0.4.2-2-gaa88037" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" package_config: name: "demultiplex" - version: "v0.4.2" + version: "v0.4.3" description: "Demultiplexing pipeline\n" info: test_resources: @@ -238,7 +238,7 @@ package_config: )'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + - ".engines[.type == 'docker'].target_tag := 'v0.4.3'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/runner/_viash.yaml b/target/nextflow/runner/_viash.yaml index 2b1172e..9c24dd5 100644 --- a/target/nextflow/runner/_viash.yaml +++ b/target/nextflow/runner/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.4.2 +version: v0.4.3 description: | Demultiplexing pipeline license: MIT diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index a6f09a7..b3c7c36 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.4.2 +// runner v0.4.3 // // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -3031,7 +3031,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "runner", - "version" : "v0.4.2", + "version" : "v0.4.3", "argument_groups" : [ { "name" : "Input arguments", @@ -3296,13 +3296,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.4", - "git_commit" : "21de648b218d114d3ab155462f4f08f4d585f741", + "git_commit" : "aa8803720f098287518db3d2dc74eff24cf003f1", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.1.1-40-g21de648" + "git_tag" : "v0.4.2-2-gaa88037" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.4.2", + "version" : "v0.4.3", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3319,7 +3319,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.4.2'" + ".engines[.type == 'docker'].target_tag := 'v0.4.3'" ], "keywords" : [ "bioinformatics", @@ -3414,6 +3414,15 @@ workflow run_wf { println("Publising to ${params.publish_dir}/${prefix}") + // Create a file to indicate that the publishing (transfer) of files has been completed. + // Multiple items can be added to onCompleteActions; which is required when processing multiple sequencing runs at a time. + // Alternatively setOnComplete could be used to add actions, but that only adds them at the end of the list (which is executed in order). + // The 'completed.txt' file must be created before the onComplete of the integration tests are run, so we need to prepend to the list. + workflow.onCompleteActions.add(0, { + def complete_file = file("${params.publish_dir}/${prefix}/transfer_completed.txt") + complete_file.text = "" // This will create a file when it does not exist. + }) + [ input: state.output, input_sample_qc: state.output_sample_qc, diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config index 3ee62e7..658408a 100644 --- a/target/nextflow/runner/nextflow.config +++ b/target/nextflow/runner/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'runner' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.4.2' + version = 'v0.4.3' description = 'Runner for demultiplexing of raw sequencing data' }