From 194cb8d0f13e184cbe03986a9059cc1d98688bed Mon Sep 17 00:00:00 2001 From: CI Date: Wed, 14 May 2025 09:11:58 +0000 Subject: [PATCH] Build branch v0.3 with version v0.3.11 (cd2cfac) Build pipeline: viash-hub.demultiplex.v0.3-nwj5p Source commit: https://github.com/viash-hub/demultiplex/commit/cd2cfac18e14622e1a5d7a0d489f64c30e83dab2 Source message: Bump version to v0.3.11 --- CHANGELOG.md | 6 ++ README.md | 6 +- README.qmd | 6 +- _viash.yaml | 2 +- src/demultiplex/config.vsh.yaml | 5 ++ src/demultiplex/main.nf | 23 ++++-- src/demultiplex/test.nf | 32 ++++++++ src/io/interop_summary_to_csv/config.vsh.yaml | 4 + src/io/interop_summary_to_csv/test.sh | 18 +++++ src/io/publish/code.sh | 1 + src/io/publish/config.vsh.yaml | 7 ++ src/runner/config.vsh.yaml | 4 + src/runner/main.nf | 4 + .../interop_summary_to_csv/.config.vsh.yaml | 18 +++-- .../interop_summary_to_csv | 14 ++-- target/executable/io/publish/.config.vsh.yaml | 32 ++++++-- target/executable/io/publish/publish | 79 +++++++++++++++++-- target/executable/io/untar/.config.vsh.yaml | 12 +-- target/executable/io/untar/untar | 14 ++-- .../dataflow/combine_samples/.config.vsh.yaml | 10 +-- .../nextflow/dataflow/combine_samples/main.nf | 12 +-- .../dataflow/combine_samples/nextflow.config | 2 +- .../.config.vsh.yaml | 10 +-- .../gather_fastqs_and_validate/main.nf | 12 +-- .../nextflow.config | 2 +- target/nextflow/demultiplex/.config.vsh.yaml | 21 +++-- target/nextflow/demultiplex/main.nf | 48 ++++++++--- target/nextflow/demultiplex/nextflow.config | 2 +- .../nextflow/demultiplex/nextflow_schema.json | 11 +++ .../interop_summary_to_csv/.config.vsh.yaml | 18 +++-- .../io/interop_summary_to_csv/main.nf | 27 +++++-- .../io/interop_summary_to_csv/nextflow.config | 2 +- target/nextflow/io/publish/.config.vsh.yaml | 32 ++++++-- target/nextflow/io/publish/main.nf | 42 ++++++++-- target/nextflow/io/publish/nextflow.config | 2 +- .../nextflow/io/publish/nextflow_schema.json | 21 +++++ target/nextflow/io/untar/.config.vsh.yaml | 12 +-- target/nextflow/io/untar/main.nf | 16 ++-- target/nextflow/io/untar/nextflow.config | 2 +- target/nextflow/runner/.config.vsh.yaml | 21 +++-- target/nextflow/runner/main.nf | 29 +++++-- target/nextflow/runner/nextflow.config | 2 +- target/nextflow/runner/nextflow_schema.json | 11 +++ 43 files changed, 501 insertions(+), 153 deletions(-) create mode 100644 src/io/interop_summary_to_csv/test.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index 2b619f9..c83ef66 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# demultiplex v0.3.11 + +# New features + +* Output demultiplexer logs and metrics (PR #41). + # demultiplex v0.3.10 ## Minor changes diff --git a/README.md b/README.md index dc078e1..ee95a20 100644 --- a/README.md +++ b/README.md @@ -153,7 +153,7 @@ workflow: ``` bash nextflow run \ vsh/demultiplex \ --r v0.3.9 \ +-r v0.3.11 \ --help ``` @@ -165,7 +165,7 @@ instance using the following: ``` bash nextflow run vsh/demultiplex \ - -revision v0.3.9 \ + -revision v0.3.11 \ -main-script target/nextflow/workflows/runner/main.nf \ --help ``` @@ -175,7 +175,7 @@ command: ``` bash nextflow run vsh/demultiplex \ --r v0.3.9 \ +-r v0.3.11 \ -main-script target/nextflow/runner/main.nf \ --input "gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2" \ --demultiplexer bclconvert \ diff --git a/README.qmd b/README.qmd index 1aecf7e..2eba38d 100644 --- a/README.qmd +++ b/README.qmd @@ -129,7 +129,7 @@ You can check if everything is working by getting the `--help` for a workflow: ```bash nextflow run \ vsh/demultiplex \ --r v0.3.9 \ +-r v0.3.11 \ --help ``` @@ -141,7 +141,7 @@ using the following: ``` bash nextflow run vsh/demultiplex \ - -revision v0.3.9 \ + -revision v0.3.11 \ -main-script target/nextflow/workflows/runner/main.nf \ --help ``` @@ -150,7 +150,7 @@ Having this project available locally, you can run the following command: ```bash nextflow run vsh/demultiplex \ --r v0.3.9 \ +-r v0.3.11 \ -main-script target/nextflow/runner/main.nf \ --input "gs://viash-hub-resources/demultiplex/v3/demultiplex_htrnaseq_meta/SingleCell-RNA_P3_2" \ --demultiplexer bclconvert \ diff --git a/_viash.yaml b/_viash.yaml index a5ce1e7..a5ab3eb 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.3.10 +version: v0.3.11 description: | Demultiplexing pipeline license: MIT diff --git a/src/demultiplex/config.vsh.yaml b/src/demultiplex/config.vsh.yaml index f3466c4..ea77de3 100644 --- a/src/demultiplex/config.vsh.yaml +++ b/src/demultiplex/config.vsh.yaml @@ -54,6 +54,11 @@ argument_groups: direction: "output" required: true default: "$id/run_information.csv" + - name: "--demultiplexer_logs" + type: file + direction: output + required: true + default: "$id/demultiplexer_logs" - name: "Other arguments" arguments: - name: --skip_copycomplete_check diff --git a/src/demultiplex/main.nf b/src/demultiplex/main.nf index 3592e33..5748338 100644 --- a/src/demultiplex/main.nf +++ b/src/demultiplex/main.nf @@ -124,14 +124,15 @@ workflow run_wf { bcl_input_directory: state.input, sample_sheet: state.run_information, output_directory: state.output, - reports: "reports", - logs: "logs" + reports: state.demultiplexer_logs, + logs: state.demultiplexer_logs, ] }, toState: {id, result, state -> def toAdd = [ "output_demultiplexer" : result.output_directory, "run_id": id, + "demultiplexer_logs": result.reports, ] def newState = state + toAdd return newState @@ -141,11 +142,15 @@ workflow run_wf { | bases2fastq.run( runIf: {id, state -> state.demultiplexer in ["bases2fastq"]}, directives: [label: ["highmem", "midcpu"]], - fromState: [ - "analysis_directory": "input", - "run_manifest": "run_information", - "output_directory": "output", - ], + fromState: { id, state -> + [ + "analysis_directory": state.input, + "run_manifest": state.run_information, + "output_directory": state.output, + "report": state.demultiplexer_logs + "/report.html", + "logs": state.demultiplexer_logs, + ] + }, args: [ "no_projects": true, // Do not put output files in a subfolder for project //"split_lanes": true, @@ -156,6 +161,8 @@ workflow run_wf { def toAdd = [ "output_demultiplexer" : result.output_directory, "run_id": id, + "demultiplexer_logs": result.logs, + ] def newState = state + toAdd return newState @@ -225,6 +232,7 @@ workflow run_wf { state + [ "output_multiqc" : result.output_report ] } ) + | setState( [ //"_meta": "_meta", @@ -232,6 +240,7 @@ workflow run_wf { "output_falco": "output_falco", "output_multiqc": "output_multiqc", "output_run_information": "run_information", + "demultiplexer_logs": "demultiplexer_logs" ] ) diff --git a/src/demultiplex/test.nf b/src/demultiplex/test.nf index a21d60d..64a54bf 100644 --- a/src/demultiplex/test.nf +++ b/src/demultiplex/test.nf @@ -23,6 +23,14 @@ workflow test_illumina { assert output.size() == 2 : "outputs should contain two elements; [id, file]" "Output: $output" } + + event_count_ch = output_ch + | toSortedList() + | map { state -> + assert state.size() == 1 : "Expected one event in the output channel" + } + + assert_ch = output_ch | map {id, state -> assert state.output.isDirectory(): "Expected bclconvert output to be a directory" state.output_falco.each{ @@ -57,6 +65,21 @@ workflow test_illumina { |1,sampletest,PatientSample,UDP0004,ATTCCATAAG,TGCCTGGTGG |""".stripMargin() assert state.output_run_information.text.replaceAll("\r\n", "\n") == expected_run_information + + println "ID: ${id}" + println "State: ${state}" + + assert state.demultiplexer_logs.isDirectory(): + "Expected BCL Convert reports to be a directory" + + def logs_files = state.demultiplexer_logs.listFiles() + println "Logs files: ${logs_files}" + assert logs_files.size() > 0: "Expected BCL Convert logs dir to contain files" + + assert logs_files.find { it.name == "Demultiplex_Stats.csv" }: + "Expected to find BCL Convert Demultiplex_Stats.csv" + assert logs_files.find { it.name == "Logs" }: + "Expected to find BCL Convert Logs directory" } } @@ -80,5 +103,14 @@ workflow test_bases2fastq { assert state.output.isDirectory(): "Expected bases2fastq output to be a directory" state.output_falco.each{assert it.isDirectory(): "Expected falco output to be a directory"} assert state.output_multiqc.isFile(): "Expected multiQC output to be a file" + + def logs_files = state.demultiplexer_logs.listFiles() + println "Logs files: ${logs_files}" + assert logs_files.size() > 0: "Expected bases2fastq logs dir to contain files" + + assert logs_files.find { it.name == "report.html" } != null: + "Expected to find bases2fastq report.html" + assert logs_files.find { it.name == "info" }: + "Expected to find bases2fastq info directory" } } diff --git a/src/io/interop_summary_to_csv/config.vsh.yaml b/src/io/interop_summary_to_csv/config.vsh.yaml index 853ae89..7ed3b8e 100644 --- a/src/io/interop_summary_to_csv/config.vsh.yaml +++ b/src/io/interop_summary_to_csv/config.vsh.yaml @@ -22,6 +22,10 @@ requirements: resources: - type: bash_script path: script.sh +test_resources: + - type: bash_script + path: test.sh + - path: /testData/iseq-DI engines: - type: docker image: debian:stable-slim diff --git a/src/io/interop_summary_to_csv/test.sh b/src/io/interop_summary_to_csv/test.sh new file mode 100644 index 0000000..d0ba9ce --- /dev/null +++ b/src/io/interop_summary_to_csv/test.sh @@ -0,0 +1,18 @@ +#!/usr/bin/env bash + +set -eo pipefail + +# create tempdir +echo ">>> Creating temporary test directory." +TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX") +function clean_up { + [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR" +} +trap clean_up EXIT +echo ">>> Created temporary directory '$TMPDIR'." + +echo ">>> Run simple execution" +./$meta_functionality_name \ + --input "$meta_resources_dir/iseq-DI" \ + --output_run_summary "$TMPDIR/run_summary.csv" \ + --output_index_summary "$TMPDIR/index_summary.csv" \ No newline at end of file diff --git a/src/io/publish/code.sh b/src/io/publish/code.sh index 54f0b31..b4a8914 100755 --- a/src/io/publish/code.sh +++ b/src/io/publish/code.sh @@ -5,6 +5,7 @@ set -eo pipefail declare -A input_output_mapping=(["par_input"]="par_output" ["par_input_multiqc"]="par_output_multiqc" ["par_input_run_information"]="par_output_run_information" + ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs" ) for input_argument_name in "${!input_output_mapping[@]}" diff --git a/src/io/publish/config.vsh.yaml b/src/io/publish/config.vsh.yaml index 3410b26..c41c257 100644 --- a/src/io/publish/config.vsh.yaml +++ b/src/io/publish/config.vsh.yaml @@ -21,6 +21,9 @@ argument_groups: description: "Location where to write the run information to." type: file required: true + - name: "--input_demultiplexer_logs" + type: file + required: true - name: Output arguments arguments: - name: --output @@ -39,6 +42,10 @@ argument_groups: type: file direction: output default: run_information.csv + - name: "--output_demultiplexer_logs" + type: file + direction: output + default: "demultiplexer_logs" resources: - type: bash_script diff --git a/src/runner/config.vsh.yaml b/src/runner/config.vsh.yaml index 5359d54..9f3cd37 100644 --- a/src/runner/config.vsh.yaml +++ b/src/runner/config.vsh.yaml @@ -49,6 +49,10 @@ argument_groups: type: file direction: output default: "qc/multiqc_report.html" + - name: "--demultiplexer_logs" + type: file + direction: output + default: "demultiplexer_logs" - name: "Other arguments" arguments: - name: --skip_copycomplete_check diff --git a/src/runner/main.nf b/src/runner/main.nf index 8cc7802..9ee0b0e 100644 --- a/src/runner/main.nf +++ b/src/runner/main.nf @@ -28,6 +28,7 @@ workflow run_wf { "output": "$id/fastq", "output_falco": "$id/qc/fastqc", "output_multiqc": "$id/qc/multiqc_report.html", + "demultiplexer_logs": "$id/demultiplexer_logs", ] if (state.run_information) { state_to_pass += ["output_run_information": state.run_information.getName()] @@ -48,6 +49,7 @@ workflow run_wf { def falco_output_1 = (id2 == "run") ? state.falco_output : "${id2}/" + state.falco_output def multiqc_output_1 = (id2 == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output def run_information_output_1 = (id2 == "run") ? "${state.output_run_information.getName()}" : "${id2}/${state.output_run_information.getName()}" + def demultiplexer_logs_output = (id2 == "run") ? state.demultiplexer_logs : "${id2}/${state.demultiplexer_logs.getName()}" if (id2 == "run") { println("Publising to ${params.publish_dir}") @@ -60,10 +62,12 @@ workflow run_wf { input_falco: state.output_falco, input_multiqc: state.output_multiqc, input_run_information: state.output_run_information, + input_demultiplexer_logs: state.demultiplexer_logs, output: fastq_output_1, output_falco: falco_output_1, output_multiqc: multiqc_output_1, output_run_information: run_information_output_1, + output_demultiplexer_logs: demultiplexer_logs_output, ] }, toState: { id, result, state -> [:] }, 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 71e6a67..446c3ae 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -41,6 +41,12 @@ resources: - type: "file" path: "nextflow_labels.config" dest: "nextflow_labels.config" +test_resources: +- type: "bash_script" + path: "test.sh" + is_executable: true +- type: "file" + path: "iseq-DI" info: null status: "enabled" scope: @@ -126,7 +132,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.10" + target_tag: "v0.3.11" namespace_separator: "/" setup: - type: "apt" @@ -151,12 +157,12 @@ 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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -172,7 +178,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" 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 dd4b9b3..9c6e843 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 v0.3.10 +# interop_summary_to_csv v0.3.11 # # 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="2025-05-07T11:20:11Z" +LABEL org.opencontainers.image.created="2025-05-14T08:46:02Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" -LABEL org.opencontainers.image.version="v0.3.10" +LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" +LABEL org.opencontainers.image.version="v0.3.11" 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 v0.3.10" + echo "interop_summary_to_csv v0.3.11" echo "" echo "Input arguments:" echo " --input" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "interop_summary_to_csv v0.3.10" + echo "interop_summary_to_csv v0.3.11" exit ;; --input) @@ -759,7 +759,7 @@ if [[ "$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:v0.3.10' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.11' fi # print dockerfile diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index de24598..82ddc06 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -44,6 +44,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--input_demultiplexer_logs" + info: null + must_exist: true + create_parent: true + required: true + direction: "input" + multiple: false + multiple_sep: ";" - name: "Output arguments" arguments: - type: "file" @@ -90,6 +99,17 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--output_demultiplexer_logs" + info: null + default: + - "demultiplexer_logs" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "code.sh" @@ -181,7 +201,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.10" + target_tag: "v0.3.11" namespace_separator: "/" setup: - type: "apt" @@ -199,12 +219,12 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -220,7 +240,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 19b138e..d24d9c9 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish v0.3.10 +# publish v0.3.11 # # 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="2025-05-07T11:20:10Z" +LABEL org.opencontainers.image.created="2025-05-14T08:46:03Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" -LABEL org.opencontainers.image.version="v0.3.10" +LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" +LABEL org.opencontainers.image.version="v0.3.11" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish v0.3.10" + echo "publish v0.3.11" echo "" echo "Publish the processed results of the run" echo "" @@ -591,6 +591,9 @@ function ViashHelp { echo " type: file, required parameter, file must exist" echo " Location where to write the run information to." echo "" + echo " --input_demultiplexer_logs" + echo " type: file, required parameter, file must exist" + echo "" echo "Output arguments:" echo " --output" echo " type: file, output, file must exist" @@ -608,6 +611,10 @@ function ViashHelp { echo " type: file, output, file must exist" echo " default: run_information.csv" echo "" + echo " --output_demultiplexer_logs" + echo " type: file, output, file must exist" + echo " default: demultiplexer_logs" + echo "" echo "Viash built in Computational Requirements:" echo " ---cpus=INT" echo " Number of CPUs to use" @@ -655,7 +662,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish v0.3.10" + echo "publish v0.3.11" exit ;; --input) @@ -708,6 +715,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1") shift 1 ;; + --input_demultiplexer_logs) + [ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --input_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --input_demultiplexer_logs=*) + [ -n "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--input_demultiplexer_logs=*\': \'$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1") + shift 1 + ;; --output) [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT="$2" @@ -752,6 +770,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashRemoveFlags "$1") shift 1 ;; + --output_demultiplexer_logs) + [ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --output_demultiplexer_logs. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --output_demultiplexer_logs=*) + [ -n "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && ViashError Bad arguments for option \'--output_demultiplexer_logs=*\': \'$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashRemoveFlags "$1") + shift 1 + ;; ---engine) VIASH_ENGINE_ID="$2" shift 2 @@ -840,7 +869,7 @@ if [[ "$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:v0.3.10' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.11' fi # print dockerfile @@ -940,6 +969,10 @@ if [ -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then ViashError '--input_run_information' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi +if [ -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then + ViashError '--input_demultiplexer_logs' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi if [ -z ${VIASH_META_NAME+x} ]; then ViashError 'name' is a required argument. Use "--help" to get more information on the parameters. exit 1 @@ -978,6 +1011,9 @@ fi if [ -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then VIASH_PAR_OUTPUT_RUN_INFORMATION="run_information.csv" fi +if [ -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then + VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS="demultiplexer_logs" +fi # check whether required files exist if [ ! -z "$VIASH_PAR_INPUT" ] && [ ! -e "$VIASH_PAR_INPUT" ]; then @@ -1004,6 +1040,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_INPUT_RUN_I ViashError "Input file '$VIASH_PAR_INPUT_RUN_INFORMATION' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then + ViashError "Input file '$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS' does not exist." + exit 1 +fi # check whether parameters values are of the right type if [[ -n "$VIASH_META_CPUS" ]]; then @@ -1092,6 +1132,9 @@ fi if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")" ]; then mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_RUN_INFORMATION")" fi +if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" +fi if [ "$VIASH_ENGINE_ID" == "native" ] ; then if [ "$VIASH_MODE" == "run" ]; then @@ -1128,6 +1171,10 @@ if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_RUN_INFORMATION")" ) VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_RUN_INFORMATION") fi +if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS")" ) + VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS") +fi if [ ! -z "$VIASH_PAR_OUTPUT" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT")" ) VIASH_PAR_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT") @@ -1148,6 +1195,11 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_RUN_INFORMATION") VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ) fi +if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS")" ) + VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ) +fi if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" ) VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR") @@ -1221,10 +1273,12 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#' $( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi ) $( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi ) $( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi ) +$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\"'\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\"'\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\"'\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -1252,6 +1306,7 @@ set -eo pipefail declare -A input_output_mapping=(["par_input"]="par_output" ["par_input_multiqc"]="par_output_multiqc" ["par_input_run_information"]="par_output_run_information" + ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs" ) for input_argument_name in "\${!input_output_mapping[@]}" @@ -1310,6 +1365,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_INPUT_RUN_INFORMATION" ]; then VIASH_PAR_INPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_RUN_INFORMATION") fi + if [ ! -z "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS" ]; then + VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS") + fi if [ ! -z "$VIASH_PAR_OUTPUT" ]; then VIASH_PAR_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT") fi @@ -1322,6 +1380,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ]; then VIASH_PAR_OUTPUT_RUN_INFORMATION=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_RUN_INFORMATION") fi + if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then + VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS=$(ViashDockerStripAutomount "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS") + fi if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR") fi @@ -1354,6 +1415,10 @@ if [ ! -z "$VIASH_PAR_OUTPUT_RUN_INFORMATION" ] && [ ! -e "$VIASH_PAR_OUTPUT_RUN ViashError "Output file '$VIASH_PAR_OUTPUT_RUN_INFORMATION' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ] && [ ! -e "$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS" ]; then + ViashError "Output file '$VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS' does not exist." + exit 1 +fi exit 0 diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 21cdef7..10674e1 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -138,7 +138,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.10" + target_tag: "v0.3.11" namespace_separator: "/" setup: - type: "apt" @@ -156,12 +156,12 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -177,7 +177,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index ef3e904..4e89be9 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# untar v0.3.10 +# untar v0.3.11 # # 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="2025-05-07T11:20:10Z" +LABEL org.opencontainers.image.created="2025-05-14T08:46:02Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" -LABEL org.opencontainers.image.version="v0.3.10" +LABEL org.opencontainers.image.revision="cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" +LABEL org.opencontainers.image.version="v0.3.11" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "untar v0.3.10" + echo "untar v0.3.11" echo "" echo "Unpack a .tar file. When the contents of the .tar file is just a single" echo "directory," @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "untar v0.3.10" + echo "untar v0.3.11" exit ;; --input) @@ -771,7 +771,7 @@ if [[ "$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:v0.3.10' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.11' fi # print dockerfile diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index ae9478b..ea1df00 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -165,12 +165,12 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -186,7 +186,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 2967e22..c547091 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -1,4 +1,4 @@ -// combine_samples v0.3.10 +// combine_samples v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3230,13 +3230,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3253,7 +3253,7 @@ 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", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config index 302f2e5..4a0d92c 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 = 'v0.3.10' + version = 'v0.3.11' 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 fec95a6..b881f04 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -141,12 +141,12 @@ 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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -162,7 +162,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" 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 ae4c56f..c46eec0 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 v0.3.10 +// gather_fastqs_and_validate v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3203,13 +3203,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3226,7 +3226,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config index 0cdc090..0e2475d 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/gather_fastqs_and_validate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.10' + version = 'v0.3.11' description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n' } diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 4612c0e..d72689e 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "demultiplex" -version: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -96,6 +96,17 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--demultiplexer_logs" + info: null + default: + - "$id/demultiplexer_logs" + must_exist: true + create_parent: true + required: true + direction: "output" + multiple: false + multiple_sep: ";" - name: "Other arguments" arguments: - type: "boolean_true" @@ -247,9 +258,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" @@ -261,7 +272,7 @@ build_info: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -277,7 +288,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index b6be472..0a8c556 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -1,4 +1,4 @@ -// demultiplex v0.3.10 +// demultiplex v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3139,6 +3139,19 @@ meta = [ "direction" : "output", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--demultiplexer_logs", + "default" : [ + "$id/demultiplexer_logs" + ], + "must_exist" : true, + "create_parent" : true, + "required" : true, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3350,13 +3363,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3373,7 +3386,7 @@ meta = [ ".requirements.commands += ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", @@ -3530,14 +3543,15 @@ workflow run_wf { bcl_input_directory: state.input, sample_sheet: state.run_information, output_directory: state.output, - reports: "reports", - logs: "logs" + reports: state.demultiplexer_logs, + logs: state.demultiplexer_logs, ] }, toState: {id, result, state -> def toAdd = [ "output_demultiplexer" : result.output_directory, "run_id": id, + "demultiplexer_logs": result.reports, ] def newState = state + toAdd return newState @@ -3547,11 +3561,15 @@ workflow run_wf { | bases2fastq.run( runIf: {id, state -> state.demultiplexer in ["bases2fastq"]}, directives: [label: ["highmem", "midcpu"]], - fromState: [ - "analysis_directory": "input", - "run_manifest": "run_information", - "output_directory": "output", - ], + fromState: { id, state -> + [ + "analysis_directory": state.input, + "run_manifest": state.run_information, + "output_directory": state.output, + "report": state.demultiplexer_logs + "/report.html", + "logs": state.demultiplexer_logs, + ] + }, args: [ "no_projects": true, // Do not put output files in a subfolder for project //"split_lanes": true, @@ -3562,6 +3580,8 @@ workflow run_wf { def toAdd = [ "output_demultiplexer" : result.output_directory, "run_id": id, + "demultiplexer_logs": result.logs, + ] def newState = state + toAdd return newState @@ -3631,6 +3651,7 @@ workflow run_wf { state + [ "output_multiqc" : result.output_report ] } ) + | setState( [ //"_meta": "_meta", @@ -3638,6 +3659,7 @@ workflow run_wf { "output_falco": "output_falco", "output_multiqc": "output_multiqc", "output_run_information": "run_information", + "demultiplexer_logs": "demultiplexer_logs" ] ) diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config index 7d0733e..e8d5b0a 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 = 'v0.3.10' + version = 'v0.3.11' description = 'Demultiplexing of raw sequencing data' } diff --git a/target/nextflow/demultiplex/nextflow_schema.json b/target/nextflow/demultiplex/nextflow_schema.json index 9c010c2..bc8b65e 100644 --- a/target/nextflow/demultiplex/nextflow_schema.json +++ b/target/nextflow/demultiplex/nextflow_schema.json @@ -109,6 +109,17 @@ } + , + "demultiplexer_logs": { + "type": + "string", + "description": "Type: `file`, required, default: `$id/demultiplexer_logs`. ", + "help_text": "Type: `file`, required, default: `$id/demultiplexer_logs`. " + , + "default":"$id/demultiplexer_logs" + } + + } }, 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 fcd4573..dc819c4 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -41,6 +41,12 @@ resources: - type: "file" path: "nextflow_labels.config" dest: "nextflow_labels.config" +test_resources: +- type: "bash_script" + path: "test.sh" + is_executable: true +- type: "file" + path: "iseq-DI" info: null status: "enabled" scope: @@ -126,7 +132,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.10" + target_tag: "v0.3.11" namespace_separator: "/" setup: - type: "apt" @@ -151,12 +157,12 @@ 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: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -172,7 +178,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" 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 8278626..76bd018 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 v0.3.10 +// interop_summary_to_csv v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3088,6 +3088,17 @@ meta = [ "dest" : "nextflow_labels.config" } ], + "test_resources" : [ + { + "type" : "bash_script", + "path" : "test.sh", + "is_executable" : true + }, + { + "type" : "file", + "path" : "/testData/iseq-DI" + } + ], "status" : "enabled", "scope" : { "image" : "public", @@ -3187,7 +3198,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.10", + "target_tag" : "v0.3.11", "namespace_separator" : "/", "setup" : [ { @@ -3217,13 +3228,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3240,7 +3251,7 @@ 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", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", @@ -3684,7 +3695,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/interop_summary_to_csv", - "tag" : "v0.3.10" + "tag" : "v0.3.11" }, "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 97a43cd..8a5e1ab 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 = 'v0.3.10' + version = 'v0.3.11' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 0d974ee..8f9aa18 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -44,6 +44,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--input_demultiplexer_logs" + info: null + must_exist: true + create_parent: true + required: true + direction: "input" + multiple: false + multiple_sep: ";" - name: "Output arguments" arguments: - type: "file" @@ -90,6 +99,17 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--output_demultiplexer_logs" + info: null + default: + - "demultiplexer_logs" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" resources: - type: "bash_script" path: "code.sh" @@ -181,7 +201,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.10" + target_tag: "v0.3.11" namespace_separator: "/" setup: - type: "apt" @@ -199,12 +219,12 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -220,7 +240,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 77835ff..077b21f 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -1,4 +1,4 @@ -// publish v0.3.10 +// publish v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3080,6 +3080,16 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--input_demultiplexer_logs", + "must_exist" : true, + "create_parent" : true, + "required" : true, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3137,6 +3147,19 @@ meta = [ "direction" : "output", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--output_demultiplexer_logs", + "default" : [ + "demultiplexer_logs" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" } ] } @@ -3251,7 +3274,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.10", + "target_tag" : "v0.3.11", "namespace_separator" : "/", "setup" : [ { @@ -3274,13 +3297,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3297,7 +3320,7 @@ 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", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", @@ -3330,10 +3353,12 @@ $( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#' $( if [ ! -z ${VIASH_PAR_INPUT_FALCO+x} ]; then echo "${VIASH_PAR_INPUT_FALCO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_falco='&'#" ; else echo "# par_input_falco="; fi ) $( if [ ! -z ${VIASH_PAR_INPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_INPUT_MULTIQC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_multiqc='&'#" ; else echo "# par_input_multiqc="; fi ) $( if [ ! -z ${VIASH_PAR_INPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_INPUT_RUN_INFORMATION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_run_information='&'#" ; else echo "# par_input_run_information="; fi ) +$( if [ ! -z ${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_INPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_input_demultiplexer_logs='&'#" ; else echo "# par_input_demultiplexer_logs="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "${VIASH_PAR_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output='&'#" ; else echo "# par_output="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_FALCO+x} ]; then echo "${VIASH_PAR_OUTPUT_FALCO}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_falco='&'#" ; else echo "# par_output_falco="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_MULTIQC+x} ]; then echo "${VIASH_PAR_OUTPUT_MULTIQC}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_multiqc='&'#" ; else echo "# par_output_multiqc="; fi ) $( if [ ! -z ${VIASH_PAR_OUTPUT_RUN_INFORMATION+x} ]; then echo "${VIASH_PAR_OUTPUT_RUN_INFORMATION}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_run_information='&'#" ; else echo "# par_output_run_information="; fi ) +$( if [ ! -z ${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS+x} ]; then echo "${VIASH_PAR_OUTPUT_DEMULTIPLEXER_LOGS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_output_demultiplexer_logs='&'#" ; else echo "# par_output_demultiplexer_logs="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi ) @@ -3361,6 +3386,7 @@ set -eo pipefail declare -A input_output_mapping=(["par_input"]="par_output" ["par_input_multiqc"]="par_output_multiqc" ["par_input_run_information"]="par_output_run_information" + ["par_input_demultiplexer_logs"]="par_output_demultiplexer_logs" ) for input_argument_name in "\\${!input_output_mapping[@]}" @@ -3769,7 +3795,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/publish", - "tag" : "v0.3.10" + "tag" : "v0.3.11" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config index a74033c..825352d 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 = 'v0.3.10' + version = 'v0.3.11' description = 'Publish the processed results of the run' } diff --git a/target/nextflow/io/publish/nextflow_schema.json b/target/nextflow/io/publish/nextflow_schema.json index 7a2bb38..7433f60 100644 --- a/target/nextflow/io/publish/nextflow_schema.json +++ b/target/nextflow/io/publish/nextflow_schema.json @@ -53,6 +53,16 @@ } + , + "input_demultiplexer_logs": { + "type": + "string", + "description": "Type: `file`, required. ", + "help_text": "Type: `file`, required. " + + } + + } }, @@ -107,6 +117,17 @@ } + , + "output_demultiplexer_logs": { + "type": + "string", + "description": "Type: `file`, default: `demultiplexer_logs`. ", + "help_text": "Type: `file`, default: `demultiplexer_logs`. " + , + "default":"demultiplexer_logs" + } + + } }, diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index ba6d95c..fe4eaea 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: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -138,7 +138,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.10" + target_tag: "v0.3.11" namespace_separator: "/" setup: - type: "apt" @@ -156,12 +156,12 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -177,7 +177,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 032802a..5c60d00 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -1,4 +1,4 @@ -// untar v0.3.10 +// untar v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3204,7 +3204,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.10", + "target_tag" : "v0.3.11", "namespace_separator" : "/", "setup" : [ { @@ -3227,13 +3227,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3250,7 +3250,7 @@ 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", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", @@ -3724,7 +3724,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/untar", - "tag" : "v0.3.10" + "tag" : "v0.3.11" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config index 46710d1..030bc7f 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 = 'v0.3.10' + version = 'v0.3.11' 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 762c4ab..bf369fd 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "runner" -version: "v0.3.10" +version: "v0.3.11" argument_groups: - name: "Input arguments" arguments: @@ -84,6 +84,17 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--demultiplexer_logs" + info: null + default: + - "demultiplexer_logs" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - name: "Other arguments" arguments: - type: "boolean_true" @@ -195,15 +206,15 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.4" - git_commit: "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6" + git_commit: "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.10" + git_tag: "v0.3.10-5-gcd2cfac" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" package_config: name: "demultiplex" - version: "v0.3.10" + version: "v0.3.11" description: "Demultiplexing pipeline\n" info: test_resources: @@ -219,7 +230,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.11'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index a38bf4c..71a0305 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.3.10 +// runner v0.3.11 // // 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" : "v0.3.10", + "version" : "v0.3.11", "argument_groups" : [ { "name" : "Input arguments", @@ -3125,6 +3125,19 @@ meta = [ "direction" : "output", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--demultiplexer_logs", + "default" : [ + "demultiplexer_logs" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3270,13 +3283,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.4", - "git_commit" : "e6fbd0c2203f8ddda7f737ea22a113bd7be10fa6", + "git_commit" : "cd2cfac18e14622e1a5d7a0d489f64c30e83dab2", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.10" + "git_tag" : "v0.3.10-5-gcd2cfac" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.10", + "version" : "v0.3.11", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3293,7 +3306,7 @@ 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", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.10'" + ".engines[.type == 'docker'].target_tag := 'v0.3.11'" ], "keywords" : [ "bioinformatics", @@ -3348,6 +3361,7 @@ workflow run_wf { "output": "$id/fastq", "output_falco": "$id/qc/fastqc", "output_multiqc": "$id/qc/multiqc_report.html", + "demultiplexer_logs": "$id/demultiplexer_logs", ] if (state.run_information) { state_to_pass += ["output_run_information": state.run_information.getName()] @@ -3368,6 +3382,7 @@ workflow run_wf { def falco_output_1 = (id2 == "run") ? state.falco_output : "${id2}/" + state.falco_output def multiqc_output_1 = (id2 == "run") ? state.multiqc_output : "${id2}/" + state.multiqc_output def run_information_output_1 = (id2 == "run") ? "${state.output_run_information.getName()}" : "${id2}/${state.output_run_information.getName()}" + def demultiplexer_logs_output = (id2 == "run") ? state.demultiplexer_logs : "${id2}/${state.demultiplexer_logs.getName()}" if (id2 == "run") { println("Publising to ${params.publish_dir}") @@ -3380,10 +3395,12 @@ workflow run_wf { input_falco: state.output_falco, input_multiqc: state.output_multiqc, input_run_information: state.output_run_information, + input_demultiplexer_logs: state.demultiplexer_logs, output: fastq_output_1, output_falco: falco_output_1, output_multiqc: multiqc_output_1, output_run_information: run_information_output_1, + output_demultiplexer_logs: demultiplexer_logs_output, ] }, toState: { id, result, state -> [:] }, diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config index 426d080..891d844 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 = 'v0.3.10' + version = 'v0.3.11' description = 'Runner for demultiplexing of raw sequencing data' } diff --git a/target/nextflow/runner/nextflow_schema.json b/target/nextflow/runner/nextflow_schema.json index 5c79973..5aa7ffa 100644 --- a/target/nextflow/runner/nextflow_schema.json +++ b/target/nextflow/runner/nextflow_schema.json @@ -109,6 +109,17 @@ } + , + "demultiplexer_logs": { + "type": + "string", + "description": "Type: `file`, default: `demultiplexer_logs`. ", + "help_text": "Type: `file`, default: `demultiplexer_logs`. " + , + "default":"demultiplexer_logs" + } + + } },