From e5ae6d3bb5c0568f85724e080feb07064659f332 Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 11 Dec 2024 18:07:49 +0000 Subject: [PATCH] Build branch v0.3 with version v0.3.2 (7ad45f3) Build pipeline: viash-hub.demultiplex.v0.3-92c55 Source commit: https://github.com/viash-hub/demultiplex/commit/7ad45f359753205547f96df54ee07733ece655e1 Source message: Bump version to 0.3.2 --- CHANGELOG.md | 6 ++++++ _viash.yaml | 2 +- .../gather_fastqs_and_validate/main.nf | 5 ++++- .../interop_summary_to_csv/.config.vsh.yaml | 14 +++++++------- .../interop_summary_to_csv | 14 +++++++------- target/executable/io/publish/.config.vsh.yaml | 14 +++++++------- target/executable/io/publish/publish | 14 +++++++------- target/executable/io/untar/.config.vsh.yaml | 14 +++++++------- target/executable/io/untar/untar | 14 +++++++------- .../dataflow/combine_samples/.config.vsh.yaml | 12 ++++++------ .../nextflow/dataflow/combine_samples/main.nf | 14 +++++++------- .../dataflow/combine_samples/nextflow.config | 2 +- .../.config.vsh.yaml | 12 ++++++------ .../gather_fastqs_and_validate/main.nf | 19 +++++++++++-------- .../nextflow.config | 2 +- target/nextflow/demultiplex/.config.vsh.yaml | 12 ++++++------ target/nextflow/demultiplex/main.nf | 14 +++++++------- target/nextflow/demultiplex/nextflow.config | 2 +- .../interop_summary_to_csv/.config.vsh.yaml | 14 +++++++------- .../io/interop_summary_to_csv/main.nf | 18 +++++++++--------- .../io/interop_summary_to_csv/nextflow.config | 2 +- target/nextflow/io/publish/.config.vsh.yaml | 14 +++++++------- target/nextflow/io/publish/main.nf | 18 +++++++++--------- target/nextflow/io/publish/nextflow.config | 2 +- target/nextflow/io/untar/.config.vsh.yaml | 14 +++++++------- target/nextflow/io/untar/main.nf | 18 +++++++++--------- target/nextflow/io/untar/nextflow.config | 2 +- target/nextflow/runner/.config.vsh.yaml | 12 ++++++------ target/nextflow/runner/main.nf | 14 +++++++------- target/nextflow/runner/nextflow.config | 2 +- 30 files changed, 164 insertions(+), 152 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9aa01b6..3bb38b9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# demultiplex v0.3.2 + +# Bug fixes + +* Ignore empty CSV entries when parsing sample information (PR #29). + # demultiplex v0.3.1 # Minor updates diff --git a/_viash.yaml b/_viash.yaml index 94e0dd5..c32d473 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.3.1 +version: v0.3.2 description: | Demultiplexing pipeline license: MIT diff --git a/src/dataflow/gather_fastqs_and_validate/main.nf b/src/dataflow/gather_fastqs_and_validate/main.nf index ce8b90f..76c5d60 100644 --- a/src/dataflow/gather_fastqs_and_validate/main.nf +++ b/src/dataflow/gather_fastqs_and_validate/main.nf @@ -50,7 +50,10 @@ workflow run_wf { println "Found sample names column '${csv_items[sample_id_column_index]}'." return } - samples += csv_items[sample_id_column_index] + def candidate_sample_id = csv_items[sample_id_column_index] + if (candidate_sample_id?.trim()) { // Don't add empty csv entries. + samples += csv_items[sample_id_column_index] + } } // This return is important! (If 'true' is returned, the parsing stops.) return diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml index 05ee353..fc82fab 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -116,7 +116,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.1" + target_tag: "v0.3.2" namespace_separator: "/" setup: - type: "apt" @@ -141,12 +141,12 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -160,7 +160,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" 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 bfd43df..8a98e19 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 v0.3.1 +# interop_summary_to_csv v0.3.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "interop_summary_to_csv v0.3.1" + echo "interop_summary_to_csv v0.3.2" echo "" echo "Input arguments:" echo " --input" @@ -470,10 +470,10 @@ 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="2024-12-11T15:30:29Z" +LABEL org.opencontainers.image.created="2024-12-11T17:51:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9" -LABEL org.opencontainers.image.version="v0.3.1" +LABEL org.opencontainers.image.revision="7ad45f359753205547f96df54ee07733ece655e1" +LABEL org.opencontainers.image.version="v0.3.2" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "interop_summary_to_csv v0.3.1" + echo "interop_summary_to_csv v0.3.2" exit ;; --input) @@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.2' fi # print dockerfile diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index 6e2e9f9..29ce3ac 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -152,7 +152,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.1" + target_tag: "v0.3.2" namespace_separator: "/" setup: - type: "apt" @@ -170,12 +170,12 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -189,7 +189,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 83d2853..8cc3218 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish v0.3.1 +# publish v0.3.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish v0.3.1" + echo "publish v0.3.2" echo "" echo "Publish the processed results of the run" echo "" @@ -482,10 +482,10 @@ 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="2024-12-11T15:30:29Z" +LABEL org.opencontainers.image.created="2024-12-11T17:51:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9" -LABEL org.opencontainers.image.version="v0.3.1" +LABEL org.opencontainers.image.revision="7ad45f359753205547f96df54ee07733ece655e1" +LABEL org.opencontainers.image.version="v0.3.2" VIASHDOCKER fi @@ -621,7 +621,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish v0.3.1" + echo "publish v0.3.2" exit ;; --input) @@ -778,7 +778,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.2' fi # print dockerfile diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 1fd2284..1482715 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -130,7 +130,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.1" + target_tag: "v0.3.2" namespace_separator: "/" setup: - type: "apt" @@ -148,12 +148,12 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -167,7 +167,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index 94cd5de..7db4f20 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# untar v0.3.1 +# untar v0.3.2 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "untar v0.3.1" + echo "untar v0.3.2" echo "" echo "Unpack a .tar file. When the contents of the .tar file is just a single" echo "directory," @@ -476,10 +476,10 @@ 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="2024-12-11T15:30:29Z" +LABEL org.opencontainers.image.created="2024-12-11T17:51:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="35e1ab8495ccf6345443da0d8e09f56fc89da8f9" -LABEL org.opencontainers.image.version="v0.3.1" +LABEL org.opencontainers.image.revision="7ad45f359753205547f96df54ee07733ece655e1" +LABEL org.opencontainers.image.version="v0.3.2" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "untar v0.3.1" + echo "untar v0.3.2" exit ;; --input) @@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.1' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.2' fi # print dockerfile diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index a5b0897..79de487 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_samples" namespace: "dataflow" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -139,12 +139,12 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -158,7 +158,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index e342acd..73bcc31 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -1,4 +1,4 @@ -// combine_samples v0.3.1 +// combine_samples v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_samples", "namespace" : "dataflow", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -2972,13 +2972,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -2995,7 +2995,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config index 31130ca..05a029d 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 = 'v0.3.1' + version = 'v0.3.2' 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 3401978..1800dc4 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: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -133,12 +133,12 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -152,7 +152,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index 0df9a0a..3705e02 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 v0.3.1 +// gather_fastqs_and_validate v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "gather_fastqs_and_validate", "namespace" : "dataflow", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -2965,13 +2965,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -2988,7 +2988,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", @@ -3063,7 +3063,10 @@ workflow run_wf { println "Found sample names column '${csv_items[sample_id_column_index]}'." return } - samples += csv_items[sample_id_column_index] + def candidate_sample_id = csv_items[sample_id_column_index] + if (candidate_sample_id?.trim()) { // Don't add empty csv entries. + samples += csv_items[sample_id_column_index] + } } // This return is important! (If 'true' is returned, the parsing stops.) return diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config index 45e35a2..10e622e 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 = 'v0.3.1' + version = 'v0.3.2' 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 2fda917..0fb2af3 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "demultiplex" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -220,9 +220,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" @@ -234,7 +234,7 @@ build_info: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -248,7 +248,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index af530bb..5a38a3e 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -1,4 +1,4 @@ -// demultiplex v0.3.1 +// demultiplex v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -3088,13 +3088,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3111,7 +3111,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config index f959936..8550437 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 = 'v0.3.1' + version = 'v0.3.2' description = 'Demultiplexing of raw sequencing data' } 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 a311cc9..a3308f5 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: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -116,7 +116,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.1" + target_tag: "v0.3.2" namespace_separator: "/" setup: - type: "apt" @@ -141,12 +141,12 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -160,7 +160,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index 88edee6..398deec 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 v0.3.1 +// interop_summary_to_csv v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "interop_summary_to_csv", "namespace" : "io", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -2947,7 +2947,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.1", + "target_tag" : "v0.3.2", "namespace_separator" : "/", "setup" : [ { @@ -2977,13 +2977,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3000,7 +3000,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", @@ -3423,7 +3423,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/interop_summary_to_csv", - "tag" : "v0.3.1" + "tag" : "v0.3.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config index c68b6c5..689bc7d 100644 --- a/target/nextflow/io/interop_summary_to_csv/nextflow.config +++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/interop_summary_to_csv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.1' + version = 'v0.3.2' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index d47dbe6..2e41c76 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -152,7 +152,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.1" + target_tag: "v0.3.2" namespace_separator: "/" setup: - type: "apt" @@ -170,12 +170,12 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -189,7 +189,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 34a010d..d8d6f75 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -1,4 +1,4 @@ -// publish v0.3.1 +// publish v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish", "namespace" : "io", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -2989,7 +2989,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.1", + "target_tag" : "v0.3.2", "namespace_separator" : "/", "setup" : [ { @@ -3012,13 +3012,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3035,7 +3035,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", @@ -3481,7 +3481,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/publish", - "tag" : "v0.3.1" + "tag" : "v0.3.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config index 5ee7d97..81050d5 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 = 'v0.3.1' + version = 'v0.3.2' 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 f9ded9d..51d77fc 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: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -130,7 +130,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.1" + target_tag: "v0.3.2" namespace_separator: "/" setup: - type: "apt" @@ -148,12 +148,12 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -167,7 +167,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index b4eabf0..f77aab4 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -1,4 +1,4 @@ -// untar v0.3.1 +// untar v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "untar", "namespace" : "io", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -2966,7 +2966,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.1", + "target_tag" : "v0.3.2", "namespace_separator" : "/", "setup" : [ { @@ -2989,13 +2989,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3012,7 +3012,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", @@ -3465,7 +3465,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/untar", - "tag" : "v0.3.1" + "tag" : "v0.3.2" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config index c8eeca1..fa8e3a1 100644 --- a/target/nextflow/io/untar/nextflow.config +++ b/target/nextflow/io/untar/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/untar' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.1' + version = 'v0.3.2' description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n' } diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 30548a1..c821b93 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "runner" -version: "v0.3.1" +version: "v0.3.2" argument_groups: - name: "Input arguments" arguments: @@ -182,15 +182,15 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.0" - git_commit: "35e1ab8495ccf6345443da0d8e09f56fc89da8f9" - git_remote: "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex" - git_tag: "v0.3.0-4-g35e1ab8" + git_commit: "7ad45f359753205547f96df54ee07733ece655e1" + git_remote: "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex" + git_tag: "v0.3.1-3-g7ad45f3" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" package_config: name: "demultiplex" - version: "v0.3.1" + version: "v0.3.2" description: "Demultiplexing pipeline\n" info: test_resources: @@ -204,7 +204,7 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.2'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 8b39ca3..92e1e83 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.3.1 +// runner v0.3.2 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "runner", - "version" : "v0.3.1", + "version" : "v0.3.2", "argument_groups" : [ { "name" : "Input arguments", @@ -3027,13 +3027,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.0", - "git_commit" : "35e1ab8495ccf6345443da0d8e09f56fc89da8f9", - "git_remote" : "https://x-access-token:ghs_dmJWFAeqmuLT7KwI3AQx37VetEueKn4JL2Vx@github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.0-4-g35e1ab8" + "git_commit" : "7ad45f359753205547f96df54ee07733ece655e1", + "git_remote" : "https://x-access-token:ghs_Yd3of90BXneMupSK4qIbEdGLmCGJet1c95Fo@github.com/viash-hub/demultiplex", + "git_tag" : "v0.3.1-3-g7ad45f3" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.1", + "version" : "v0.3.2", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3050,7 +3050,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.1'" + ".engines[.type == 'docker'].target_tag := 'v0.3.2'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config index 198d7c4..ae4b47d 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 = 'v0.3.1' + version = 'v0.3.2' description = 'Runner for demultiplexing of raw sequencing data' }