From 6f76b494680f736c16a7fbbdb07e6131e5c8fe8d Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 1 Aug 2025 10:14:18 +0000 Subject: [PATCH] Build branch main with version main (10d3b38) Build pipeline: viash-hub.htrnaseq.main-77sg6 Source commit: https://github.com/viash-hub/htrnaseq/commit/10d3b382d6ee8368c846736f24b076eeddfc8ce2 Source message: Add runner integration tests, revert ec0dd8b (#64) --- CHANGELOG.md | 16 ++ src/workflows/runner/config.vsh.yaml | 12 +- src/workflows/runner/integration_test.sh | 13 ++ src/workflows/runner/main.nf | 31 +-- src/workflows/runner/nextflow.config | 4 + src/workflows/runner/test.nf | 181 ++++++++++++++++++ .../eset/create_eset/.config.vsh.yaml | 4 +- .../executable/eset/create_eset/create_eset | 4 +- .../eset/create_fdata/.config.vsh.yaml | 4 +- .../executable/eset/create_fdata/create_fdata | 4 +- .../eset/create_pdata/.config.vsh.yaml | 4 +- .../executable/eset/create_pdata/create_pdata | 4 +- .../htrnaseq/check_eset/.config.vsh.yaml | 4 +- .../htrnaseq/check_eset/check_eset | 4 +- .../check_cutadapt_output/.config.vsh.yaml | 4 +- .../check_cutadapt_output | 4 +- .../io/publish_fastqs/.config.vsh.yaml | 4 +- .../io/publish_fastqs/publish_fastqs | 4 +- .../io/publish_results/.config.vsh.yaml | 4 +- .../io/publish_results/publish_results | 4 +- .../executable/parallel_map/.config.vsh.yaml | 4 +- target/executable/parallel_map/parallel_map | 4 +- .../report/create_report/.config.vsh.yaml | 4 +- .../report/create_report/create_report | 4 +- .../stats/combine_star_logs/.config.vsh.yaml | 4 +- .../stats/combine_star_logs/combine_star_logs | 4 +- .../generate_pool_statistics/.config.vsh.yaml | 4 +- .../generate_pool_statistics | 4 +- .../generate_well_statistics/.config.vsh.yaml | 4 +- .../generate_well_statistics | 4 +- .../utils/save_params/.config.vsh.yaml | 4 +- .../executable/utils/save_params/save_params | 4 +- .../eset/create_eset/.config.vsh.yaml | 4 +- target/nextflow/eset/create_eset/main.nf | 4 +- .../eset/create_fdata/.config.vsh.yaml | 4 +- target/nextflow/eset/create_fdata/main.nf | 4 +- .../eset/create_pdata/.config.vsh.yaml | 4 +- target/nextflow/eset/create_pdata/main.nf | 4 +- .../htrnaseq/check_eset/.config.vsh.yaml | 4 +- .../htrnaseq/check_eset/main.nf | 4 +- .../check_cutadapt_output/.config.vsh.yaml | 4 +- .../check_cutadapt_output/main.nf | 4 +- .../io/publish_fastqs/.config.vsh.yaml | 4 +- target/nextflow/io/publish_fastqs/main.nf | 4 +- .../io/publish_results/.config.vsh.yaml | 4 +- target/nextflow/io/publish_results/main.nf | 4 +- target/nextflow/parallel_map/.config.vsh.yaml | 4 +- target/nextflow/parallel_map/main.nf | 4 +- .../report/create_report/.config.vsh.yaml | 4 +- target/nextflow/report/create_report/main.nf | 4 +- .../stats/combine_star_logs/.config.vsh.yaml | 4 +- .../nextflow/stats/combine_star_logs/main.nf | 4 +- .../generate_pool_statistics/.config.vsh.yaml | 4 +- .../stats/generate_pool_statistics/main.nf | 4 +- .../generate_well_statistics/.config.vsh.yaml | 4 +- .../stats/generate_well_statistics/main.nf | 4 +- .../utils/concatRuns/.config.vsh.yaml | 4 +- target/nextflow/utils/concatRuns/main.nf | 4 +- .../utils/listInputDir/.config.vsh.yaml | 4 +- target/nextflow/utils/listInputDir/main.nf | 4 +- .../utils/save_params/.config.vsh.yaml | 4 +- target/nextflow/utils/save_params/main.nf | 4 +- .../workflows/htrnaseq/.config.vsh.yaml | 4 +- target/nextflow/workflows/htrnaseq/main.nf | 4 +- .../workflows/runner/.config.vsh.yaml | 17 +- target/nextflow/workflows/runner/main.nf | 52 ++--- .../workflows/runner/nextflow_schema.json | 16 -- .../well_demultiplex/.config.vsh.yaml | 4 +- .../workflows/well_demultiplex/main.nf | 4 +- .../workflows/well_metadata/.config.vsh.yaml | 4 +- .../nextflow/workflows/well_metadata/main.nf | 4 +- 71 files changed, 373 insertions(+), 217 deletions(-) create mode 100755 src/workflows/runner/integration_test.sh create mode 100644 src/workflows/runner/test.nf diff --git a/CHANGELOG.md b/CHANGELOG.md index 030670b8..a93a43fa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,19 @@ +# htrnaseq v0.9.1 + +## Bug fixes + +* Reverted functionality to set `fastq_publish_dir` and `results_publish_dir` using fromState (PR #64). + +# htrnaseq v0.9.0 + +## Breaking changes + +* `runner`: removed `plain_output` argument (PR #63). + +## Minor changes + +* `runner`: the `fastq_publish_dir` and `results_publish_dir` can now be set using `fromState` when using the workflow as subworkflow (PR #63). + # htrnaseq v0.8.3 ## Minor changes diff --git a/src/workflows/runner/config.vsh.yaml b/src/workflows/runner/config.vsh.yaml index df788ba6..0dc1ba94 100644 --- a/src/workflows/runner/config.vsh.yaml +++ b/src/workflows/runner/config.vsh.yaml @@ -46,13 +46,6 @@ argument_groups: description: Experiment ID type: string required: true - - name: Annotation flags - arguments: - - name: --plain_output - description: | - Flag to indicate that the output should be stored directly under $publish_dir rather than - under a subdirectory structure runID/_demultiplex_/. - type: boolean_true - name: Publish arguments arguments: - name: --fastq_publish_dir @@ -67,6 +60,11 @@ resources: path: main.nf entrypoint: run_wf +test_resources: + - type: nextflow_script + path: test.nf + entrypoint: test_wf + dependencies: - name: utils/listInputDir repository: local diff --git a/src/workflows/runner/integration_test.sh b/src/workflows/runner/integration_test.sh new file mode 100755 index 00000000..aa69cb73 --- /dev/null +++ b/src/workflows/runner/integration_test.sh @@ -0,0 +1,13 @@ +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +nextflow \ + run . \ + -main-script src/workflows/runner/test.nf \ + -config ./src/config/labels.config \ + -entry test_wf \ + -resume \ + -profile docker,local diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index b9e99bc9..b9254e0e 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -157,20 +157,10 @@ workflow run_wf { results_publish_ch = grouped_with_params_list_ch | publish_results.run( fromState: { id, state -> - def project = (state.plain_output) ? id : "${state.project_id}" - def experiment = (state.plain_output) ? id : "${state.experiment_id}" - def id0 = "${project}/${experiment}" - def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}" - def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}" - - if (id == id2) { - println("Publising results to ${params.results_publish_dir}") - } else { - println("Publising results to ${params.results_publish_dir}/${id2}") - } + def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}" + println("Publising results to ${params.results_publish_dir}/${output_dir}") [ - star_output: state.star_output, star_output: state.star_output, nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom, star_qc_metrics: state.star_qc_metrics, @@ -179,7 +169,7 @@ workflow run_wf { p_data: state.p_data, html_report: state.html_report, run_params: state.run_params, - output: "${id2}" + output: output_dir.toString() ] }, toState: { id, result, state -> state }, @@ -210,19 +200,12 @@ workflow run_wf { } | publish_fastqs.run( fromState: { id, state -> - def id0 = state.run_id - def id1 = (state.plain_output) ? id : "${id0}/${date}" - def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}/${state.sample_id}" - - if (id == id2) { - println("Publising fastqs to ${params.fastq_publish_dir}") - } else { - println("Publising fastqs to ${params.fastq_publish_dir}/${id2}") - } + def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}" + println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}") [ input: state.fastq_output, - output: "${id2}", + output: output_dir.toString(), ] }, toState: { id, result, state -> state }, @@ -279,4 +262,4 @@ def reduce_paths(paths, offset = 0) { println("") return grouped_paths -} +} \ No newline at end of file diff --git a/src/workflows/runner/nextflow.config b/src/workflows/runner/nextflow.config index 20297b81..1c43d0d6 100644 --- a/src/workflows/runner/nextflow.config +++ b/src/workflows/runner/nextflow.config @@ -2,6 +2,10 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() +} + process { withName: publishStatesProc { publishDir = [ enabled: false ] diff --git a/src/workflows/runner/test.nf b/src/workflows/runner/test.nf new file mode 100644 index 00000000..523fe529 --- /dev/null +++ b/src/workflows/runner/test.nf @@ -0,0 +1,181 @@ +import java.nio.file.Files +import nextflow.exception.WorkflowScriptErrorException + +def viash_config = java.nio.file.Paths.get("${params.rootDir}/target/nextflow/workflows/runner/_viash.yaml") + +def get_version(inputFile) { + def yamlSlurper = new groovy.yaml.YamlSlurper() + def loaded_viash_config = yamlSlurper.parse(file(inputFile)) + def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version" + println("HT-RNAseq version to be used: ${version}") + return version +} + +// Create temporary directory for the publish_dir if it is not defined +if (!params.containsKey("publish_dir") && params.containsKey("publishDir")) { + params.publish_dir = params.publishDir +} + +if (!params.containsKey("publish_dir")) { + def tempDir = Files.createTempDirectory("demultiplex_runner_integration_test") + println "Created temp directory: $tempDir" + // Register shutdown hook to delete it on JVM exit + Runtime.runtime.addShutdownHook(new Thread({ + try { + // Delete directory recursively + Files.walk(tempDir) + .sorted(Comparator.reverseOrder()) + .forEach { Files.delete(it) } + println "Deleted temp directory: $tempDir" + } catch (Exception e) { + println "Failed to delete temp directory: $e" + } + })) + params.publish_dir = tempDir +} + +params.fastq_publish_dir = (file(params.publish_dir) / "fastq").toUriString() +params.results_publish_dir = (file(params.publish_dir) / "results").toUriString() + + +// The module inherits the parameters defined before the include statement, +// therefore any parameters set afterwards will not be used by the module. + +include { runner } from params.rootDir + "/target/nextflow/workflows/runner/main.nf" +params.resources_test = params.rootDir + "/resources_test" + +workflow test_wf { + pipeline_version = get_version(viash_config) + resources_test = file(params.resources_test) + + // results_publish_dir and results_publish_dir are inherited using params + // but they must be defined in the state as well because viash will check + // if all arguments are present in the hashmap + output_ch = Channel.fromList([ + [ + id: "run_1", + input: resources_test.resolve("10k/SRR14730301"), + genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"), + barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"), + annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"), + project_id: "foo", + experiment_id: "bar", + fastq_publish_dir: params.fastq_publish_dir, + results_publish_dir: params.results_publish_dir, + ], + [ + id: "run_2", + input: resources_test.resolve("10k/SRR14730301"), + genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"), + barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"), + annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"), + project_id: "foo", + experiment_id: "bar", + fastq_publish_dir: params.fastq_publish_dir, + results_publish_dir: params.results_publish_dir, + ], + [ + id: "run_3", + input:resources_test.resolve("10k/SRR14730302"), + genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"), + barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"), + annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"), + project_id: "foo", + experiment_id: "bar", + fastq_publish_dir: params.fastq_publish_dir, + results_publish_dir: params.results_publish_dir, + ] + ]) + | map { state -> [state.id, state]} + | runner.run( + toState: { id, output, state -> output + [orig_input: state.input] } + ) + | view { output -> + assert output.size() == 2 : "outputs should contain two elements; [id, file]" + "Output: $output" + } + + tosortedlistch = output_ch + | toSortedList() + | map {events -> + assert events.size() == 1, "Expected one events to be output, found ${events.size()}" + } + + + workflow.onComplete = { + try { + // Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException). + // So in order for the assert statement to work (or allow other errors to let the tests to fail) + // We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files + // The error message will show up in .nextflow.log + def fastq_subdir = file("${params.fastq_publish_dir}") + assert fastq_subdir.isDirectory() + def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet() + def expected_run_folders = ["run_1", "run_2", "run_3"].toSet() + assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}" + unique_dirs = [ + "run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'), + "run2": files("${fastq_subdir.toUriString()}/run_2/*_htrnaseq_${pipeline_version}", type: 'any'), + "run3": files("${fastq_subdir.toUriString()}/run_3/*_htrnaseq_${pipeline_version}", type: 'any'), + ] + assert unique_dirs.every{it.value.size() == 1} + unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]} + + assert unique_dirs.every{it.value.isDirectory()} + assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1 + def expected_samples = [ + "run1": "VH02001612", + "run2": "VH02001612", + "run3": "VH02001614" + ] + + unique_dirs.each{_key, _value -> + def expected_sample = expected_samples[_key] + def expected_sample_dir = _value.resolve(expected_sample) + assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}" + def expected_fastq_files = [ + "A1_R1_001.fastq", "A1_R2_001.fastq", + "B1_R1_001.fastq", "B1_R2_001.fastq", + "unknown_R1_001.fastq", "unknown_R2_001.fastq"] + def found_files = files("${expected_sample_dir}/*.fastq", type: 'any') + assert found_files.every{it.isFile()} + assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet() + } + + def results_subdir = file("${params.results_publish_dir}") + assert fastq_subdir.isDirectory() + def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any') + assert expected_subdir.isDirectory() + def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any') + assert expected_result_dir.size() == 1 + expected_result_dir = expected_result_dir[0] + assert expected_result_dir.isDirectory() + def expected_esets = ["VH02001612.rds", "VH02001614.rds"] + def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any') + assert found_esets.size() == 2 + assert found_esets.collect{it.name}.toSet() == expected_esets.toSet() + expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"] + def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any') + assert found_pdata.size() == 2 + assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet() + def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any') + assert found_nr_genes_nr_reads.size() == 2 + assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet() + def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any') + assert found_star_logs.size() == 2 + assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet() + def star_output = file("${expected_result_dir}/star_output", type: 'any') + assert star_output.isDirectory() + + assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet() + assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet() + assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet() + assert file("${expected_result_dir}/report.html").isFile() + assert file("${expected_result_dir}/params.yaml").isFile() + assert file("${expected_result_dir}/fData.gencode.v41.annotation.gtf.gz.txt").isFile() + + } catch (Exception e) { + throw new WorkflowScriptErrorException("Integration test failed!", e) + } + } +} diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index 4fe5d524..dd944a1d 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -206,9 +206,9 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index 171fa031..13b2a5a4 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -456,9 +456,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_eset" -LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 5fdc2566..022dd4e5 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 9d4d2188..5e0dc11c 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:58Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index fd1fc3bb..44cb2ad0 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -197,9 +197,9 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index a5b19404..c828ebac 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 39d673ff..6da61921 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -155,9 +155,9 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset index 98ab7bbb..5df1c2e0 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -455,9 +455,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset" -LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:58Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index db53f4e7..27f13945 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -164,9 +164,9 @@ build_info: output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output index adb4c3e3..c3cf32b2 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:58Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index b18e0a0e..084fed81 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -139,9 +139,9 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index 340bcc79..758fcf92 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -450,9 +450,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs" -LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 3debb478..8edafebe 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -202,9 +202,9 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 34f2a0f5..c9ed3062 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -450,9 +450,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish_results" -LABEL org.opencontainers.image.created="2025-07-29T10:37:43Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index eb59816f..5d397bd6 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -285,9 +285,9 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index a3cc7724..0ca87be2 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -461,9 +461,9 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-07-29T10:37:44Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 2221e638..f02fa5a7 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -215,9 +215,9 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index e37cf633..e03424e8 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -465,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component report create_report" -LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 90b2daeb..2ef2c556 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -204,9 +204,9 @@ build_info: output: "target/executable/stats/combine_star_logs" executable: "target/executable/stats/combine_star_logs/combine_star_logs" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index a0c65729..c284e10d 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -457,9 +457,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index f2974c4c..4c63d009 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -188,9 +188,9 @@ build_info: output: "target/executable/stats/generate_pool_statistics" executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 2a9e1759..f8fdf593 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -458,9 +458,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index 6d3b6460..de15daff 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -270,9 +270,9 @@ build_info: output: "target/executable/stats/generate_well_statistics" executable: "target/executable/stats/generate_well_statistics/generate_well_statistics" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index 5a24a6f7..7147a610 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -461,9 +461,9 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:57Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml index e41e465e..f1709899 100644 --- a/target/executable/utils/save_params/.config.vsh.yaml +++ b/target/executable/utils/save_params/.config.vsh.yaml @@ -151,9 +151,9 @@ build_info: output: "target/executable/utils/save_params" executable: "target/executable/utils/save_params/save_params" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params index a862350a..dd54856d 100755 --- a/target/executable/utils/save_params/save_params +++ b/target/executable/utils/save_params/save_params @@ -453,9 +453,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "pyyaml" LABEL org.opencontainers.image.description="Companion container for running component utils save_params" -LABEL org.opencontainers.image.created="2025-07-29T10:37:42Z" +LABEL org.opencontainers.image.created="2025-08-01T09:22:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="0e87de80bc86053b22c7105a9d24e245bd4c3160" +LABEL org.opencontainers.image.revision="10d3b382d6ee8368c846736f24b076eeddfc8ce2" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 6d840ae7..2e0b42c6 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -206,9 +206,9 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index e21b67e1..3a0cfcbc 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -3309,9 +3309,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index c16cf799..b240def8 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -183,9 +183,9 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index 025abb47..53cafbe4 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -3279,9 +3279,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index bda4c069..80603e09 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -197,9 +197,9 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index f4da5444..d1c8e5c1 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -3293,9 +3293,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 68950bfd..7fd6d6f4 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -155,9 +155,9 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf index 4d5f2750..f11c0ade 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -3233,9 +3233,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 47869c71..39603d6f 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -164,9 +164,9 @@ build_info: output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf index 5bc7ba0e..316a6ae0 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -3244,9 +3244,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index 30029d5b..ff5a830d 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -139,9 +139,9 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 73715f0d..d2f1a60a 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -3207,9 +3207,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index 31fbd4df..b7e0b6fa 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -202,9 +202,9 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index 9b675978..fdcabf3d 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -3277,9 +3277,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index c91923a9..6af2ebe4 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -285,9 +285,9 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 4742a837..25022f83 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -3379,9 +3379,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 5f449a0a..1e72f3da 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -215,9 +215,9 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index 44f5ec95..11bab234 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -3323,9 +3323,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index f4d88886..9dd79712 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -204,9 +204,9 @@ build_info: output: "target/nextflow/stats/combine_star_logs" executable: "target/nextflow/stats/combine_star_logs/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index abc0b5df..37832f5a 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -3295,9 +3295,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index 1f40784a..a79873fb 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -188,9 +188,9 @@ build_info: output: "target/nextflow/stats/generate_pool_statistics" executable: "target/nextflow/stats/generate_pool_statistics/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index b7370a92..d8a184b7 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -3279,9 +3279,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index a5ba998c..36b68764 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -270,9 +270,9 @@ build_info: output: "target/nextflow/stats/generate_well_statistics" executable: "target/nextflow/stats/generate_well_statistics/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index bddc228c..56133612 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -3374,9 +3374,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml index 8ccd0adb..bd567fc4 100644 --- a/target/nextflow/utils/concatRuns/.config.vsh.yaml +++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml @@ -160,9 +160,9 @@ build_info: output: "target/nextflow/utils/concatRuns" executable: "target/nextflow/utils/concatRuns/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" dependencies: - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text" package_config: diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf index 0ecceb69..a537de93 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -3229,9 +3229,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index f2430848..725e60ff 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -171,9 +171,9 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index b9a13590..2bc5ee2d 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -3239,9 +3239,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml index 016952cc..db487a58 100644 --- a/target/nextflow/utils/save_params/.config.vsh.yaml +++ b/target/nextflow/utils/save_params/.config.vsh.yaml @@ -151,9 +151,9 @@ build_info: output: "target/nextflow/utils/save_params" executable: "target/nextflow/utils/save_params/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf index 10cf4df2..c13b8633 100644 --- a/target/nextflow/utils/save_params/main.nf +++ b/target/nextflow/utils/save_params/main.nf @@ -3223,9 +3223,9 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/utils/save_params", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index c229ac32..9d3d2abe 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -345,9 +345,9 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" dependencies: - "target/nextflow/stats/combine_star_logs" - "target/nextflow/stats/generate_pool_statistics" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index d31999b9..dc3dd1c7 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -3484,9 +3484,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index f5a919da..1f9ee3f2 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -99,14 +99,6 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" -- name: "Annotation flags" - arguments: - - type: "boolean_true" - name: "--plain_output" - description: "Flag to indicate that the output should be stored directly under\ - \ $publish_dir rather than\nunder a subdirectory structure runID/_demultiplex_/.\n" - info: null - direction: "input" - name: "Publish arguments" arguments: - type: "string" @@ -135,6 +127,11 @@ resources: path: "_viash.yaml" dest: "_viash.yaml" description: "Runner for HT RNA-seq pipeline" +test_resources: +- type: "nextflow_script" + path: "test.nf" + is_executable: true + entrypoint: "test_wf" info: null status: "enabled" scope: @@ -238,9 +235,9 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" dependencies: - "target/nextflow/utils/listInputDir" - "target/nextflow/workflows/htrnaseq" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index 883b6276..6a0023b5 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -3150,17 +3150,6 @@ meta = [ } ] }, - { - "name" : "Annotation flags", - "arguments" : [ - { - "type" : "boolean_true", - "name" : "--plain_output", - "description" : "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/_demultiplex_/.\n", - "direction" : "input" - } - ] - }, { "name" : "Publish arguments", "arguments" : [ @@ -3202,6 +3191,14 @@ meta = [ } ], "description" : "Runner for HT RNA-seq pipeline", + "test_resources" : [ + { + "type" : "nextflow_script", + "path" : "test.nf", + "is_executable" : true, + "entrypoint" : "test_wf" + } + ], "status" : "enabled", "scope" : { "image" : "public", @@ -3336,9 +3333,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", @@ -3551,20 +3548,10 @@ workflow run_wf { results_publish_ch = grouped_with_params_list_ch | publish_results.run( fromState: { id, state -> - def project = (state.plain_output) ? id : "${state.project_id}" - def experiment = (state.plain_output) ? id : "${state.experiment_id}" - def id0 = "${project}/${experiment}" - def id1 = (state.plain_output) ? id : "${id0}/data_processed/${date}" - def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}" - - if (id == id2) { - println("Publising results to ${params.results_publish_dir}") - } else { - println("Publising results to ${params.results_publish_dir}/${id2}") - } + def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}" + println("Publising results to ${params.results_publish_dir}/${output_dir}") [ - star_output: state.star_output, star_output: state.star_output, nrReadsNrGenesPerChrom: state.nrReadsNrGenesPerChrom, star_qc_metrics: state.star_qc_metrics, @@ -3573,7 +3560,7 @@ workflow run_wf { p_data: state.p_data, html_report: state.html_report, run_params: state.run_params, - output: "${id2}" + output: output_dir.toString() ] }, toState: { id, result, state -> state }, @@ -3604,19 +3591,12 @@ workflow run_wf { } | publish_fastqs.run( fromState: { id, state -> - def id0 = state.run_id - def id1 = (state.plain_output) ? id : "${id0}/${date}" - def id2 = (state.plain_output) ? id : "${id1}_htrnaseq_${version}/${state.sample_id}" - - if (id == id2) { - println("Publising fastqs to ${params.fastq_publish_dir}") - } else { - println("Publising fastqs to ${params.fastq_publish_dir}/${id2}") - } + def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}" + println("Publising fastqs to ${params.fastq_publish_dir}/${output_dir}") [ input: state.fastq_output, - output: "${id2}", + output: output_dir.toString(), ] }, toState: { id, result, state -> state }, diff --git a/target/nextflow/workflows/runner/nextflow_schema.json b/target/nextflow/workflows/runner/nextflow_schema.json index 3e32c922..b8b2c40a 100644 --- a/target/nextflow/workflows/runner/nextflow_schema.json +++ b/target/nextflow/workflows/runner/nextflow_schema.json @@ -85,19 +85,6 @@ } } }, - "annotation flags": { - "title": "Annotation flags", - "type": "object", - "description": "No description", - "properties": { - "plain_output": { - "type": "boolean", - "description": "Flag to indicate that the output should be stored directly under $publish_dir rather than\nunder a subdirectory structure runID/_demultiplex_/.\n", - "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ", - "default": false - } - } - }, "publish arguments": { "title": "Publish arguments", "type": "object", @@ -135,9 +122,6 @@ { "$ref": "#/$defs/metadata arguments" }, - { - "$ref": "#/$defs/annotation flags" - }, { "$ref": "#/$defs/publish arguments" }, diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index b04f31f4..c9305d47 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -217,9 +217,9 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt" - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index 5b493775..a72807be 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -3319,9 +3319,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq", diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index d57e196a..951dac1a 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -215,9 +215,9 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.4" - git_commit: "0e87de80bc86053b22c7105a9d24e245bd4c3160" + git_commit: "10d3b382d6ee8368c846736f24b076eeddfc8ce2" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-9-g0e87de8" + git_tag: "v0.7.2-11-g10d3b38" package_config: name: "htrnaseq" version: "main" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index 000e1fba..51c7f076 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -3299,9 +3299,9 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.4", - "git_commit" : "0e87de80bc86053b22c7105a9d24e245bd4c3160", + "git_commit" : "10d3b382d6ee8368c846736f24b076eeddfc8ce2", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-9-g0e87de8" + "git_tag" : "v0.7.2-11-g10d3b38" }, "package_config" : { "name" : "htrnaseq",