From 843f4b7e3749e1acfd5ed743756ffc4716f0f866 Mon Sep 17 00:00:00 2001 From: CI Date: Fri, 1 Aug 2025 11:54:46 +0000 Subject: [PATCH] Build branch v0.9 with version v0.9.1 (1bce00e) Build pipeline: viash-hub.htrnaseq.v0.9-4v78w Source commit: https://github.com/viash-hub/htrnaseq/commit/1bce00e81124868b9dce7df10f3aa090ea38af22 Source message: Bump version to v0.9.1 --- CHANGELOG.md | 8 + _viash.yaml | 2 +- src/utils/listInputDir/main.nf | 2 +- src/workflows/runner/config.vsh.yaml | 5 + 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 | 12 +- .../executable/eset/create_eset/_viash.yaml | 2 +- .../executable/eset/create_eset/create_eset | 14 +- .../eset/create_fdata/.config.vsh.yaml | 12 +- .../executable/eset/create_fdata/_viash.yaml | 2 +- .../executable/eset/create_fdata/create_fdata | 14 +- .../eset/create_pdata/.config.vsh.yaml | 12 +- .../executable/eset/create_pdata/_viash.yaml | 2 +- .../executable/eset/create_pdata/create_pdata | 14 +- .../htrnaseq/check_eset/.config.vsh.yaml | 12 +- .../htrnaseq/check_eset/_viash.yaml | 2 +- .../htrnaseq/check_eset/check_eset | 14 +- .../check_cutadapt_output/.config.vsh.yaml | 12 +- .../check_cutadapt_output/_viash.yaml | 2 +- .../check_cutadapt_output | 14 +- .../io/publish_fastqs/.config.vsh.yaml | 12 +- .../executable/io/publish_fastqs/_viash.yaml | 2 +- .../io/publish_fastqs/publish_fastqs | 14 +- .../io/publish_results/.config.vsh.yaml | 12 +- .../executable/io/publish_results/_viash.yaml | 2 +- .../io/publish_results/publish_results | 14 +- .../executable/parallel_map/.config.vsh.yaml | 12 +- target/executable/parallel_map/_viash.yaml | 2 +- target/executable/parallel_map/parallel_map | 14 +- .../report/create_report/.config.vsh.yaml | 12 +- .../report/create_report/_viash.yaml | 2 +- .../report/create_report/create_report | 14 +- .../stats/combine_star_logs/.config.vsh.yaml | 12 +- .../stats/combine_star_logs/_viash.yaml | 2 +- .../stats/combine_star_logs/combine_star_logs | 14 +- .../generate_pool_statistics/.config.vsh.yaml | 12 +- .../generate_pool_statistics/_viash.yaml | 2 +- .../generate_pool_statistics | 14 +- .../generate_well_statistics/.config.vsh.yaml | 12 +- .../generate_well_statistics/_viash.yaml | 2 +- .../generate_well_statistics | 14 +- .../utils/save_params/.config.vsh.yaml | 12 +- .../executable/utils/save_params/_viash.yaml | 2 +- .../executable/utils/save_params/save_params | 14 +- .../eset/create_eset/.config.vsh.yaml | 12 +- target/nextflow/eset/create_eset/_viash.yaml | 2 +- target/nextflow/eset/create_eset/main.nf | 16 +- .../nextflow/eset/create_eset/nextflow.config | 2 +- .../eset/create_fdata/.config.vsh.yaml | 12 +- target/nextflow/eset/create_fdata/_viash.yaml | 2 +- target/nextflow/eset/create_fdata/main.nf | 16 +- .../eset/create_fdata/nextflow.config | 2 +- .../eset/create_pdata/.config.vsh.yaml | 12 +- target/nextflow/eset/create_pdata/_viash.yaml | 2 +- target/nextflow/eset/create_pdata/main.nf | 16 +- .../eset/create_pdata/nextflow.config | 2 +- .../htrnaseq/check_eset/.config.vsh.yaml | 12 +- .../htrnaseq/check_eset/_viash.yaml | 2 +- .../htrnaseq/check_eset/main.nf | 16 +- .../htrnaseq/check_eset/nextflow.config | 2 +- .../check_cutadapt_output/.config.vsh.yaml | 12 +- .../check_cutadapt_output/_viash.yaml | 2 +- .../check_cutadapt_output/main.nf | 16 +- .../check_cutadapt_output/nextflow.config | 2 +- .../io/publish_fastqs/.config.vsh.yaml | 12 +- target/nextflow/io/publish_fastqs/_viash.yaml | 2 +- target/nextflow/io/publish_fastqs/main.nf | 16 +- .../io/publish_fastqs/nextflow.config | 2 +- .../io/publish_results/.config.vsh.yaml | 12 +- .../nextflow/io/publish_results/_viash.yaml | 2 +- target/nextflow/io/publish_results/main.nf | 16 +- .../io/publish_results/nextflow.config | 2 +- target/nextflow/parallel_map/.config.vsh.yaml | 12 +- target/nextflow/parallel_map/_viash.yaml | 2 +- target/nextflow/parallel_map/main.nf | 16 +- target/nextflow/parallel_map/nextflow.config | 2 +- .../report/create_report/.config.vsh.yaml | 12 +- .../nextflow/report/create_report/_viash.yaml | 2 +- target/nextflow/report/create_report/main.nf | 16 +- .../report/create_report/nextflow.config | 2 +- .../stats/combine_star_logs/.config.vsh.yaml | 12 +- .../stats/combine_star_logs/_viash.yaml | 2 +- .../nextflow/stats/combine_star_logs/main.nf | 16 +- .../stats/combine_star_logs/nextflow.config | 2 +- .../generate_pool_statistics/.config.vsh.yaml | 12 +- .../generate_pool_statistics/_viash.yaml | 2 +- .../stats/generate_pool_statistics/main.nf | 16 +- .../generate_pool_statistics/nextflow.config | 2 +- .../generate_well_statistics/.config.vsh.yaml | 12 +- .../generate_well_statistics/_viash.yaml | 2 +- .../stats/generate_well_statistics/main.nf | 16 +- .../generate_well_statistics/nextflow.config | 2 +- .../utils/concatRuns/.config.vsh.yaml | 10 +- target/nextflow/utils/concatRuns/_viash.yaml | 2 +- target/nextflow/utils/concatRuns/main.nf | 12 +- .../nextflow/utils/concatRuns/nextflow.config | 2 +- .../utils/listInputDir/.config.vsh.yaml | 10 +- .../nextflow/utils/listInputDir/_viash.yaml | 2 +- target/nextflow/utils/listInputDir/main.nf | 14 +- .../utils/listInputDir/nextflow.config | 2 +- .../utils/save_params/.config.vsh.yaml | 12 +- target/nextflow/utils/save_params/_viash.yaml | 2 +- target/nextflow/utils/save_params/main.nf | 16 +- .../utils/save_params/nextflow.config | 2 +- .../workflows/htrnaseq/.config.vsh.yaml | 10 +- .../nextflow/workflows/htrnaseq/_viash.yaml | 2 +- target/nextflow/workflows/htrnaseq/main.nf | 12 +- .../workflows/htrnaseq/nextflow.config | 2 +- .../workflows/runner/.config.vsh.yaml | 15 +- target/nextflow/workflows/runner/_viash.yaml | 2 +- target/nextflow/workflows/runner/main.nf | 49 ++--- .../nextflow/workflows/runner/nextflow.config | 2 +- .../well_demultiplex/.config.vsh.yaml | 10 +- .../workflows/well_demultiplex/_viash.yaml | 2 +- .../workflows/well_demultiplex/main.nf | 12 +- .../well_demultiplex/nextflow.config | 2 +- .../workflows/well_metadata/.config.vsh.yaml | 10 +- .../workflows/well_metadata/_viash.yaml | 2 +- .../nextflow/workflows/well_metadata/main.nf | 12 +- .../workflows/well_metadata/nextflow.config | 2 +- 123 files changed, 700 insertions(+), 526 deletions(-) create mode 100755 src/workflows/runner/integration_test.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index 633e3888..65468195 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,11 @@ +# htrnaseq v0.9.1 + +## Bug fixes + +* Reverted functionality to set `fastq_publish_dir` and `results_publish_dir` using fromState (PR #64). + +* `runner`: fix detection of FASTQ files with non-numerical characters in the sample name (PR #65). + # htrnaseq v0.9.0 ## Breaking changes diff --git a/_viash.yaml b/_viash.yaml index 3ead1ac7..f34abce8 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: | diff --git a/src/utils/listInputDir/main.nf b/src/utils/listInputDir/main.nf index 03c97fc3..a38acb96 100644 --- a/src/utils/listInputDir/main.nf +++ b/src/utils/listInputDir/main.nf @@ -18,7 +18,7 @@ workflow run_wf { println("Extracting information from fastq/fasta filenames") def processed_fastqs = allFastqs.collect { f -> - def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/ + def regex = ~/^(\S+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/ def validFastq = f.name ==~ regex assert validFastq: "${f} does not match the regex ${regex}" diff --git a/src/workflows/runner/config.vsh.yaml b/src/workflows/runner/config.vsh.yaml index bf10aeff..0dc1ba94 100644 --- a/src/workflows/runner/config.vsh.yaml +++ b/src/workflows/runner/config.vsh.yaml @@ -60,6 +60,11 @@ resources: path: main.nf entrypoint: run_wf +test_resources: + - type: nextflow_script + path: test.nf + entrypoint: test_wf + dependencies: - name: utils/listInputDir repository: local diff --git a/src/workflows/runner/integration_test.sh b/src/workflows/runner/integration_test.sh new file mode 100755 index 00000000..aa69cb73 --- /dev/null +++ b/src/workflows/runner/integration_test.sh @@ -0,0 +1,13 @@ +# get the root of the directory +REPO_ROOT=$(git rev-parse --show-toplevel) + +# ensure that the command below is run from the root of the repository +cd "$REPO_ROOT" + +nextflow \ + run . \ + -main-script src/workflows/runner/test.nf \ + -config ./src/config/labels.config \ + -entry test_wf \ + -resume \ + -profile docker,local diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index 771b364f..b9254e0e 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -16,24 +16,6 @@ workflow run_wf { return [id, new_state] } - - // When this workflow is being used as a subworkflow, the publish directories might be defined - // in the state and not in params. The following snippets make sure the values are copied from state to params. - set_publish_dirs_channel = raw_ch - | toSortedList() - | map {ids_and_states -> - def publish_dir_arguments = ["results_publish_dir", "fastq_publish_dir"] - for (publish_dir_arg in publish_dir_arguments) { - if (!params.containsKey(publish_dir_arg)) { - def state_items = ids_and_states.collect{it[1].get(publish_dir_arg)} - assert state_items.toSet().size() == state_items.size(), "Items for '${publish_dir_arg}' must be unique! Found ${state_items}" - params[publish_dir_arg] = state_items[0] - } - } - ids_and_states - } - - save_params_ch = input_ch | toSortedList() | map { states -> @@ -172,11 +154,7 @@ workflow run_wf { } - // Use combine here in order to be sure tha the publish dirs are set in params - // set_publish_dirs_channel should contain 1 event; so the result of the combine - // contains the events from grouped_with_params_list_ch - results_publish_ch = grouped_with_params_list_ch.combine(set_publish_dirs_channel) - | map {event -> [event[0], event[1]]} + results_publish_ch = grouped_with_params_list_ch | publish_results.run( fromState: { id, state -> def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}" @@ -204,7 +182,7 @@ workflow run_wf { ] ) - fastq_publish_split_ch = grouped_ch + fastq_publish_ch = grouped_ch | flatMap{id, state -> def new_states = state.fastq_output.collect{fastq_dir -> def run_id = fastq_dir.name // The folder name corresponds to the run @@ -220,9 +198,6 @@ workflow run_wf { } return new_states } - - fastq_publish_ch = fastq_publish_split_ch.combine(set_publish_dirs_channel) - | map{event -> [event[0], event[1]]} | publish_fastqs.run( fromState: { id, state -> def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}" @@ -287,4 +262,4 @@ def reduce_paths(paths, offset = 0) { println("") return grouped_paths -} +} \ No newline at end of file diff --git a/src/workflows/runner/nextflow.config b/src/workflows/runner/nextflow.config index 20297b81..1c43d0d6 100644 --- a/src/workflows/runner/nextflow.config +++ b/src/workflows/runner/nextflow.config @@ -2,6 +2,10 @@ manifest { nextflowVersion = '!>=20.12.1-edge' } +params { + rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString() +} + process { withName: publishStatesProc { publishDir = [ enabled: false ] diff --git a/src/workflows/runner/test.nf b/src/workflows/runner/test.nf index e69de29b..523fe529 100644 --- a/src/workflows/runner/test.nf +++ 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 5143e808..1faad917 100644 --- a/target/executable/eset/create_eset/.config.vsh.yaml +++ b/target/executable/eset/create_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_eset" namespace: "eset" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "r" @@ -206,12 +206,12 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -243,7 +243,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_eset/_viash.yaml b/target/executable/eset/create_eset/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/eset/create_eset/_viash.yaml +++ b/target/executable/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/eset/create_eset/create_eset b/target/executable/eset/create_eset/create_eset index ee318ff7..07bf5864 100755 --- a/target/executable/eset/create_eset/create_eset +++ b/target/executable/eset/create_eset/create_eset @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_eset v0.9.0 +# create_eset v0.9.1 # # 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 @@ -456,10 +456,10 @@ 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="2025-07-30T14:40:41Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_eset v0.9.0" + echo "create_eset v0.9.1" echo "" echo "Arguments:" echo " --pDataFile" @@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_eset v0.9.0" + echo "create_eset v0.9.1" exit ;; --pDataFile) @@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.9.1' fi # print dockerfile diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 03c6b7e5..3e72c49c 100644 --- a/target/executable/eset/create_fdata/.config.vsh.yaml +++ b/target/executable/eset/create_fdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_fdata" namespace: "eset" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -154,7 +154,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -183,12 +183,12 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -220,7 +220,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_fdata/_viash.yaml b/target/executable/eset/create_fdata/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/eset/create_fdata/_viash.yaml +++ b/target/executable/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/eset/create_fdata/create_fdata b/target/executable/eset/create_fdata/create_fdata index 0efb42c4..23c32d71 100755 --- a/target/executable/eset/create_fdata/create_fdata +++ b/target/executable/eset/create_fdata/create_fdata @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_fdata v0.9.0 +# create_fdata v0.9.1 # # 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 @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata" -LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_fdata v0.9.0" + echo "create_fdata v0.9.1" echo "" echo "Create a fdata file" echo "" @@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_fdata v0.9.0" + echo "create_fdata v0.9.1" exit ;; --gtf) @@ -756,7 +756,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.9.1' fi # print dockerfile diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 9ec34967..817c7ae9 100644 --- a/target/executable/eset/create_pdata/.config.vsh.yaml +++ b/target/executable/eset/create_pdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pdata" namespace: "eset" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -168,7 +168,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -197,12 +197,12 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -234,7 +234,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_pdata/_viash.yaml b/target/executable/eset/create_pdata/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/eset/create_pdata/_viash.yaml +++ b/target/executable/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/eset/create_pdata/create_pdata b/target/executable/eset/create_pdata/create_pdata index ec16675c..24ee19e0 100755 --- a/target/executable/eset/create_pdata/create_pdata +++ b/target/executable/eset/create_pdata/create_pdata @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_pdata v0.9.0 +# create_pdata v0.9.1 # # 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 @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata" -LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pdata v0.9.0" + echo "create_pdata v0.9.1" echo "" echo "Create a pdata file by combining the mapping statistics" echo "" @@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pdata v0.9.0" + echo "create_pdata v0.9.1" exit ;; --star_stats_file) @@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.9.1' fi # print dockerfile diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index 3bb99289..50111601 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_eset" namespace: "integration_test_components/htrnaseq" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -134,7 +134,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "r" @@ -155,12 +155,12 @@ build_info: output: "target/executable/integration_test_components/htrnaseq/check_eset" executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -192,7 +192,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml +++ b/target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 b98e0519..6a4f03b0 100755 --- a/target/executable/integration_test_components/htrnaseq/check_eset/check_eset +++ b/target/executable/integration_test_components/htrnaseq/check_eset/check_eset @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# check_eset v0.9.0 +# check_eset v0.9.1 # # 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 @@ -455,10 +455,10 @@ 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="2025-07-30T14:40:41Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_eset v0.9.0" + echo "check_eset v0.9.1" echo "" echo "This component test the ExpressionSet object as output by the main pipeline." echo "" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_eset v0.9.0" + echo "check_eset v0.9.1" exit ;; --eset) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.9.1' fi # print dockerfile diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 7309324c..bd20b5e8 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_cutadapt_output" namespace: "integration_test_components/well_demultiplexing" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -164,12 +164,12 @@ build_info: output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -201,7 +201,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 9aae951f..643ac88a 100755 --- a/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output +++ b/target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# check_cutadapt_output v0.9.0 +# check_cutadapt_output v0.9.1 # # 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 @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output" -LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_cutadapt_output v0.9.0" + echo "check_cutadapt_output v0.9.1" echo "" echo "This component test the cutadapt output from the well_demultiplex subworkflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_cutadapt_output v0.9.0" + echo "check_cutadapt_output v0.9.1" exit ;; --fastq_r1) @@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.9.1' fi # print dockerfile diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 0b94f554..6798e06a 100644 --- a/target/executable/io/publish_fastqs/.config.vsh.yaml +++ b/target/executable/io/publish_fastqs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_fastqs" namespace: "io" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Input arguments" arguments: @@ -121,7 +121,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -139,12 +139,12 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -176,7 +176,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_fastqs/_viash.yaml b/target/executable/io/publish_fastqs/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/io/publish_fastqs/_viash.yaml +++ b/target/executable/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/io/publish_fastqs/publish_fastqs b/target/executable/io/publish_fastqs/publish_fastqs index b6d1256c..a8b2f128 100755 --- a/target/executable/io/publish_fastqs/publish_fastqs +++ b/target/executable/io/publish_fastqs/publish_fastqs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish_fastqs v0.9.0 +# publish_fastqs v0.9.1 # # 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_fastqs" -LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_fastqs v0.9.0" + echo "publish_fastqs v0.9.1" echo "" echo "Publish the fastq files per well" echo "" @@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_fastqs v0.9.0" + echo "publish_fastqs v0.9.1" exit ;; --input) @@ -750,7 +750,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.9.1' fi # print dockerfile diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 98694da4..3a83d232 100644 --- a/target/executable/io/publish_results/.config.vsh.yaml +++ b/target/executable/io/publish_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_results" namespace: "io" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Input arguments" arguments: @@ -184,7 +184,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -202,12 +202,12 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -239,7 +239,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_results/_viash.yaml b/target/executable/io/publish_results/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/io/publish_results/_viash.yaml +++ b/target/executable/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/io/publish_results/publish_results b/target/executable/io/publish_results/publish_results index 496e4da1..b8dac323 100755 --- a/target/executable/io/publish_results/publish_results +++ b/target/executable/io/publish_results/publish_results @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish_results v0.9.0 +# publish_results v0.9.1 # # 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_results" -LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_results v0.9.0" + echo "publish_results v0.9.1" echo "" echo "Publish the results" echo "" @@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_results v0.9.0" + echo "publish_results v0.9.1" exit ;; --star_output) @@ -878,7 +878,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.9.1' fi # print dockerfile diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 9aaae9a0..b130ee5f 100644 --- a/target/executable/parallel_map/.config.vsh.yaml +++ b/target/executable/parallel_map/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "parallel_map" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -285,12 +285,12 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -322,7 +322,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/parallel_map/_viash.yaml b/target/executable/parallel_map/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/parallel_map/_viash.yaml +++ b/target/executable/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/parallel_map/parallel_map b/target/executable/parallel_map/parallel_map index 713e7d6d..59ecda11 100755 --- a/target/executable/parallel_map/parallel_map +++ b/target/executable/parallel_map/parallel_map @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# parallel_map v0.9.0 +# parallel_map v0.9.1 # # 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 @@ -461,10 +461,10 @@ ENV STAR_BINARY=STAR COPY STAR /usr/local/bin/$STAR_BINARY LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren" LABEL org.opencontainers.image.description="Companion container for running component parallel_map" -LABEL org.opencontainers.image.created="2025-07-30T14:40:42Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "parallel_map v0.9.0" + echo "parallel_map v0.9.1" echo "" echo "Map wells in batch, using STAR" echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin" @@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "parallel_map v0.9.0" + echo "parallel_map v0.9.1" exit ;; --input_r1) @@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.9.1' fi # print dockerfile diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 93d96754..b308f5c2 100644 --- a/target/executable/report/create_report/.config.vsh.yaml +++ b/target/executable/report/create_report/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_report" namespace: "report" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -215,12 +215,12 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -252,7 +252,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/report/create_report/_viash.yaml b/target/executable/report/create_report/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/report/create_report/_viash.yaml +++ b/target/executable/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/report/create_report/create_report b/target/executable/report/create_report/create_report index 07fa6d1f..d5426a23 100755 --- a/target/executable/report/create_report/create_report +++ b/target/executable/report/create_report/create_report @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# create_report v0.9.0 +# create_report v0.9.1 # # 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 @@ -465,10 +465,10 @@ 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="2025-07-30T14:40:40Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_report v0.9.0" + echo "create_report v0.9.1" echo "" echo "Create a basic QC report in HTML format based on a number of esets." echo "" @@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_report v0.9.0" + echo "create_report v0.9.1" exit ;; --eset) @@ -763,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.9.1' fi # print dockerfile diff --git a/target/executable/stats/combine_star_logs/.config.vsh.yaml b/target/executable/stats/combine_star_logs/.config.vsh.yaml index 57768003..1a76c568 100644 --- a/target/executable/stats/combine_star_logs/.config.vsh.yaml +++ b/target/executable/stats/combine_star_logs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_star_logs" namespace: "stats" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -175,7 +175,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -204,12 +204,12 @@ 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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -241,7 +241,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/combine_star_logs/_viash.yaml b/target/executable/stats/combine_star_logs/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/stats/combine_star_logs/_viash.yaml +++ b/target/executable/stats/combine_star_logs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/stats/combine_star_logs/combine_star_logs b/target/executable/stats/combine_star_logs/combine_star_logs index 171ea9e2..dfeac7a2 100755 --- a/target/executable/stats/combine_star_logs/combine_star_logs +++ b/target/executable/stats/combine_star_logs/combine_star_logs @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# combine_star_logs v0.9.0 +# combine_star_logs v0.9.1 # # 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 @@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont" LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs" -LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "combine_star_logs v0.9.0" + echo "combine_star_logs v0.9.1" echo "" echo "Arguments:" echo " --barcodes" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "combine_star_logs v0.9.0" + echo "combine_star_logs v0.9.1" exit ;; --barcodes) @@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.9.1' fi # print dockerfile diff --git a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml index b35252e6..099d8132 100644 --- a/target/executable/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_pool_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_pool_statistics" namespace: "stats" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -188,12 +188,12 @@ 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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -225,7 +225,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_pool_statistics/_viash.yaml b/target/executable/stats/generate_pool_statistics/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/stats/generate_pool_statistics/_viash.yaml +++ b/target/executable/stats/generate_pool_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/stats/generate_pool_statistics/generate_pool_statistics b/target/executable/stats/generate_pool_statistics/generate_pool_statistics index 44efcc58..c5f3c93a 100755 --- a/target/executable/stats/generate_pool_statistics/generate_pool_statistics +++ b/target/executable/stats/generate_pool_statistics/generate_pool_statistics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# generate_pool_statistics v0.9.0 +# generate_pool_statistics v0.9.1 # # 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 @@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics" -LABEL org.opencontainers.image.created="2025-07-30T14:40:39Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_pool_statistics v0.9.0" + echo "generate_pool_statistics v0.9.1" echo "" echo "Arguments:" echo " --nrReadsNrGenesPerChrom" @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_pool_statistics v0.9.0" + echo "generate_pool_statistics v0.9.1" exit ;; --nrReadsNrGenesPerChrom) @@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.9.1' fi # print dockerfile diff --git a/target/executable/stats/generate_well_statistics/.config.vsh.yaml b/target/executable/stats/generate_well_statistics/.config.vsh.yaml index dac53c19..06d542fd 100644 --- a/target/executable/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/executable/stats/generate_well_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_well_statistics" namespace: "stats" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -230,7 +230,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "docker" @@ -270,12 +270,12 @@ 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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -307,7 +307,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_well_statistics/_viash.yaml b/target/executable/stats/generate_well_statistics/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/stats/generate_well_statistics/_viash.yaml +++ b/target/executable/stats/generate_well_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/stats/generate_well_statistics/generate_well_statistics b/target/executable/stats/generate_well_statistics/generate_well_statistics index 76d5887a..fed53641 100755 --- a/target/executable/stats/generate_well_statistics/generate_well_statistics +++ b/target/executable/stats/generate_well_statistics/generate_well_statistics @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# generate_well_statistics v0.9.0 +# generate_well_statistics v0.9.1 # # 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 @@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \ LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke" LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics" -LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_well_statistics v0.9.0" + echo "generate_well_statistics v0.9.1" echo "" echo "Generate summary statistics from BAM files generated by STAR solo." echo "" @@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_well_statistics v0.9.0" + echo "generate_well_statistics v0.9.1" exit ;; --input) @@ -864,7 +864,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.9.1' fi # print dockerfile diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml index d30f3b98..ba93367d 100644 --- a/target/executable/utils/save_params/.config.vsh.yaml +++ b/target/executable/utils/save_params/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "save_params" namespace: "utils" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Inputs" arguments: @@ -128,7 +128,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -151,12 +151,12 @@ build_info: output: "target/executable/utils/save_params" executable: "target/executable/utils/save_params/save_params" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -188,7 +188,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/utils/save_params/_viash.yaml b/target/executable/utils/save_params/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/executable/utils/save_params/_viash.yaml +++ b/target/executable/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/executable/utils/save_params/save_params b/target/executable/utils/save_params/save_params index 48dd3540..8acd98dd 100755 --- a/target/executable/utils/save_params/save_params +++ b/target/executable/utils/save_params/save_params @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# save_params v0.9.0 +# save_params v0.9.1 # # 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 @@ -453,10 +453,10 @@ 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="2025-07-30T14:40:40Z" +LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" -LABEL org.opencontainers.image.version="v0.9.0" +LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22" +LABEL org.opencontainers.image.version="v0.9.1" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "save_params v0.9.0" + echo "save_params v0.9.1" echo "" echo "Save parameters to a YAML file" echo "" @@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "save_params v0.9.0" + echo "save_params v0.9.1" exit ;; --id) @@ -763,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.9.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.9.1' fi # print dockerfile diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 768ef9af..0380924f 100644 --- a/target/nextflow/eset/create_eset/.config.vsh.yaml +++ b/target/nextflow/eset/create_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_eset" namespace: "eset" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -178,7 +178,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "r" @@ -206,12 +206,12 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -243,7 +243,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_eset/_viash.yaml b/target/nextflow/eset/create_eset/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/eset/create_eset/_viash.yaml +++ b/target/nextflow/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/eset/create_eset/main.nf b/target/nextflow/eset/create_eset/main.nf index 6d98b473..7dec3009 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -1,4 +1,4 @@ -// create_eset v0.9.0 +// create_eset v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_eset", "namespace" : "eset", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3271,7 +3271,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3309,13 +3309,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3333,7 +3333,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -4208,7 +4208,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_eset", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_eset/nextflow.config b/target/nextflow/eset/create_eset/nextflow.config index 920f4998..837e8975 100644 --- a/target/nextflow/eset/create_eset/nextflow.config +++ b/target/nextflow/eset/create_eset/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_eset' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/eset/create_fdata/.config.vsh.yaml b/target/nextflow/eset/create_fdata/.config.vsh.yaml index 542d0667..b6e21869 100644 --- a/target/nextflow/eset/create_fdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_fdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_fdata" namespace: "eset" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -154,7 +154,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -183,12 +183,12 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -220,7 +220,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_fdata/_viash.yaml b/target/nextflow/eset/create_fdata/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/eset/create_fdata/_viash.yaml +++ b/target/nextflow/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/eset/create_fdata/main.nf b/target/nextflow/eset/create_fdata/main.nf index ab16b92b..c439198d 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -1,4 +1,4 @@ -// create_fdata v0.9.0 +// create_fdata v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_fdata", "namespace" : "eset", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3279,13 +3279,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3303,7 +3303,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3873,7 +3873,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_fdata", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_fdata/nextflow.config b/target/nextflow/eset/create_fdata/nextflow.config index cf104e5a..7a304297 100644 --- a/target/nextflow/eset/create_fdata/nextflow.config +++ b/target/nextflow/eset/create_fdata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_fdata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Create a fdata file\n' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/eset/create_pdata/.config.vsh.yaml b/target/nextflow/eset/create_pdata/.config.vsh.yaml index 2a866d19..9a6f1d74 100644 --- a/target/nextflow/eset/create_pdata/.config.vsh.yaml +++ b/target/nextflow/eset/create_pdata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_pdata" namespace: "eset" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -168,7 +168,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -197,12 +197,12 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -234,7 +234,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_pdata/_viash.yaml b/target/nextflow/eset/create_pdata/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/eset/create_pdata/_viash.yaml +++ b/target/nextflow/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/eset/create_pdata/main.nf b/target/nextflow/eset/create_pdata/main.nf index 612f315f..3eecb85a 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -1,4 +1,4 @@ -// create_pdata v0.9.0 +// create_pdata v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_pdata", "namespace" : "eset", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3252,7 +3252,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3293,13 +3293,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3317,7 +3317,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3813,7 +3813,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_pdata", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_pdata/nextflow.config b/target/nextflow/eset/create_pdata/nextflow.config index 0c398224..7a38fd23 100644 --- a/target/nextflow/eset/create_pdata/nextflow.config +++ b/target/nextflow/eset/create_pdata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'eset/create_pdata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Create a pdata file by combining the mapping statistics \n' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml index f0e00704..dca8434c 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_eset" namespace: "integration_test_components/htrnaseq" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -134,7 +134,7 @@ engines: id: "docker" image: "bioconductor/bioconductor_docker:3.19" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "r" @@ -155,12 +155,12 @@ build_info: output: "target/nextflow/integration_test_components/htrnaseq/check_eset" executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -192,7 +192,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 839c6914..8885209e 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf @@ -1,4 +1,4 @@ -// check_eset v0.9.0 +// check_eset v0.9.1 // // 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 @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_eset", "namespace" : "integration_test_components/htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3206,7 +3206,7 @@ meta = [ "id" : "docker", "image" : "bioconductor/bioconductor_docker:3.19", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3233,13 +3233,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3257,7 +3257,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3907,7 +3907,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config index 17a38037..68b7316a 100644 --- a/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config +++ b/target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integration_test_components/htrnaseq/check_eset' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'This component test the ExpressionSet object as output by the main pipeline.' author = 'Dries Schaumont' } diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml index 3b4564ca..688bf3f3 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "check_cutadapt_output" namespace: "integration_test_components/well_demultiplexing" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -141,7 +141,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -164,12 +164,12 @@ build_info: output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output" executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -201,7 +201,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" 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 e450685f..d9752d6e 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf @@ -1,4 +1,4 @@ -// check_cutadapt_output v0.9.0 +// check_cutadapt_output v0.9.1 // // 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 @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "check_cutadapt_output", "namespace" : "integration_test_components/well_demultiplexing", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3213,7 +3213,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3244,13 +3244,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3268,7 +3268,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3787,7 +3787,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config index e840a800..af6c12e2 100644 --- a/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config +++ b/target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'integration_test_components/well_demultiplexing/check_cutadapt_output' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'This component test the cutadapt output from the well_demultiplex subworkflow.' author = 'Dries Schaumont' } diff --git a/target/nextflow/io/publish_fastqs/.config.vsh.yaml b/target/nextflow/io/publish_fastqs/.config.vsh.yaml index ea1923cd..8f5aaaad 100644 --- a/target/nextflow/io/publish_fastqs/.config.vsh.yaml +++ b/target/nextflow/io/publish_fastqs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_fastqs" namespace: "io" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Input arguments" arguments: @@ -121,7 +121,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -139,12 +139,12 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -176,7 +176,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_fastqs/_viash.yaml b/target/nextflow/io/publish_fastqs/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/io/publish_fastqs/_viash.yaml +++ b/target/nextflow/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/io/publish_fastqs/main.nf b/target/nextflow/io/publish_fastqs/main.nf index 7813e1f7..f11b412c 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -1,4 +1,4 @@ -// publish_fastqs v0.9.0 +// publish_fastqs v0.9.1 // // 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_fastqs", "namespace" : "io", - "version" : "v0.9.0", + "version" : "v0.9.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3184,7 +3184,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3207,13 +3207,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3231,7 +3231,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3683,7 +3683,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_fastqs", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_fastqs/nextflow.config b/target/nextflow/io/publish_fastqs/nextflow.config index 9483fb35..a8348ddd 100644 --- a/target/nextflow/io/publish_fastqs/nextflow.config +++ b/target/nextflow/io/publish_fastqs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_fastqs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Publish the fastq files per well' } diff --git a/target/nextflow/io/publish_results/.config.vsh.yaml b/target/nextflow/io/publish_results/.config.vsh.yaml index e192437c..6a4908b0 100644 --- a/target/nextflow/io/publish_results/.config.vsh.yaml +++ b/target/nextflow/io/publish_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish_results" namespace: "io" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Input arguments" arguments: @@ -184,7 +184,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -202,12 +202,12 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -239,7 +239,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_results/_viash.yaml b/target/nextflow/io/publish_results/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/io/publish_results/_viash.yaml +++ b/target/nextflow/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/io/publish_results/main.nf b/target/nextflow/io/publish_results/main.nf index ad2ac655..748114ce 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -1,4 +1,4 @@ -// publish_results v0.9.0 +// publish_results v0.9.1 // // 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_results", "namespace" : "io", - "version" : "v0.9.0", + "version" : "v0.9.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3254,7 +3254,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3277,13 +3277,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3301,7 +3301,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3789,7 +3789,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_results", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_results/nextflow.config b/target/nextflow/io/publish_results/nextflow.config index 05866587..f1532080 100644 --- a/target/nextflow/io/publish_results/nextflow.config +++ b/target/nextflow/io/publish_results/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_results' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Publish the results' } diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 31fa961c..c7dabef3 100644 --- a/target/nextflow/parallel_map/.config.vsh.yaml +++ b/target/nextflow/parallel_map/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "parallel_map" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -285,12 +285,12 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -322,7 +322,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/parallel_map/_viash.yaml b/target/nextflow/parallel_map/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/parallel_map/_viash.yaml +++ b/target/nextflow/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/parallel_map/main.nf b/target/nextflow/parallel_map/main.nf index 66584ffa..2c97ae4e 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -1,4 +1,4 @@ -// parallel_map v0.9.0 +// parallel_map v0.9.1 // // 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 @@ -3035,7 +3035,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "parallel_map", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3332,7 +3332,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3379,13 +3379,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3403,7 +3403,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -4172,7 +4172,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/parallel_map", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/parallel_map/nextflow.config b/target/nextflow/parallel_map/nextflow.config index be35318d..6f79c381 100644 --- a/target/nextflow/parallel_map/nextflow.config +++ b/target/nextflow/parallel_map/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'parallel_map' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n' author = 'Dries Schaumont, Toni Verbeiren' } diff --git a/target/nextflow/report/create_report/.config.vsh.yaml b/target/nextflow/report/create_report/.config.vsh.yaml index 084d2878..3ab81419 100644 --- a/target/nextflow/report/create_report/.config.vsh.yaml +++ b/target/nextflow/report/create_report/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "create_report" namespace: "report" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -215,12 +215,12 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -252,7 +252,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/report/create_report/_viash.yaml b/target/nextflow/report/create_report/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/report/create_report/_viash.yaml +++ b/target/nextflow/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/report/create_report/main.nf b/target/nextflow/report/create_report/main.nf index e3a3a5b3..dc49bae7 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -1,4 +1,4 @@ -// create_report v0.9.0 +// create_report v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "create_report", "namespace" : "report", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3251,7 +3251,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3323,13 +3323,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3347,7 +3347,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3832,7 +3832,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/report/create_report", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/create_report/nextflow.config b/target/nextflow/report/create_report/nextflow.config index f437eb34..f32ed443 100644 --- a/target/nextflow/report/create_report/nextflow.config +++ b/target/nextflow/report/create_report/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'report/create_report' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Create a basic QC report in HTML format based on a number of esets.\n' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml index 60240813..aa0a7fa9 100644 --- a/target/nextflow/stats/combine_star_logs/.config.vsh.yaml +++ b/target/nextflow/stats/combine_star_logs/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_star_logs" namespace: "stats" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -175,7 +175,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -204,12 +204,12 @@ 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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -241,7 +241,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/combine_star_logs/_viash.yaml b/target/nextflow/stats/combine_star_logs/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/stats/combine_star_logs/_viash.yaml +++ b/target/nextflow/stats/combine_star_logs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/stats/combine_star_logs/main.nf b/target/nextflow/stats/combine_star_logs/main.nf index 25c51280..5db6453a 100644 --- a/target/nextflow/stats/combine_star_logs/main.nf +++ b/target/nextflow/stats/combine_star_logs/main.nf @@ -1,4 +1,4 @@ -// combine_star_logs v0.9.0 +// combine_star_logs v0.9.1 // // 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 @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_star_logs", "namespace" : "stats", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3254,7 +3254,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3295,13 +3295,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3319,7 +3319,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3978,7 +3978,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/combine_star_logs", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/combine_star_logs/nextflow.config b/target/nextflow/stats/combine_star_logs/nextflow.config index 7802e864..fe159845 100644 --- a/target/nextflow/stats/combine_star_logs/nextflow.config +++ b/target/nextflow/stats/combine_star_logs/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/combine_star_logs' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' author = 'Dries Schaumont' } diff --git a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml index 2b365070..fc41f712 100644 --- a/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_pool_statistics" namespace: "stats" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -159,7 +159,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -188,12 +188,12 @@ 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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -225,7 +225,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_pool_statistics/_viash.yaml b/target/nextflow/stats/generate_pool_statistics/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/stats/generate_pool_statistics/_viash.yaml +++ b/target/nextflow/stats/generate_pool_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/stats/generate_pool_statistics/main.nf b/target/nextflow/stats/generate_pool_statistics/main.nf index 900cd4a2..d5461df6 100644 --- a/target/nextflow/stats/generate_pool_statistics/main.nf +++ b/target/nextflow/stats/generate_pool_statistics/main.nf @@ -1,4 +1,4 @@ -// generate_pool_statistics v0.9.0 +// generate_pool_statistics v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_pool_statistics", "namespace" : "stats", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3279,13 +3279,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3303,7 +3303,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3833,7 +3833,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_pool_statistics", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_pool_statistics/nextflow.config b/target/nextflow/stats/generate_pool_statistics/nextflow.config index 289bdc71..40935d83 100644 --- a/target/nextflow/stats/generate_pool_statistics/nextflow.config +++ b/target/nextflow/stats/generate_pool_statistics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/generate_pool_statistics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml index 68ed8140..db475b0a 100644 --- a/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml +++ b/target/nextflow/stats/generate_well_statistics/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "generate_well_statistics" namespace: "stats" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -230,7 +230,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "docker" @@ -270,12 +270,12 @@ 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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -307,7 +307,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_well_statistics/_viash.yaml b/target/nextflow/stats/generate_well_statistics/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/stats/generate_well_statistics/_viash.yaml +++ b/target/nextflow/stats/generate_well_statistics/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/stats/generate_well_statistics/main.nf b/target/nextflow/stats/generate_well_statistics/main.nf index 2fdfc057..d29a8372 100644 --- a/target/nextflow/stats/generate_well_statistics/main.nf +++ b/target/nextflow/stats/generate_well_statistics/main.nf @@ -1,4 +1,4 @@ -// generate_well_statistics v0.9.0 +// generate_well_statistics v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "generate_well_statistics", "namespace" : "stats", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3319,7 +3319,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3374,13 +3374,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3398,7 +3398,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3919,7 +3919,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_well_statistics", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_well_statistics/nextflow.config b/target/nextflow/stats/generate_well_statistics/nextflow.config index 749b5278..29424706 100644 --- a/target/nextflow/stats/generate_well_statistics/nextflow.config +++ b/target/nextflow/stats/generate_well_statistics/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stats/generate_well_statistics' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Generate summary statistics from BAM files generated by STAR solo.' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/utils/concatRuns/.config.vsh.yaml b/target/nextflow/utils/concatRuns/.config.vsh.yaml index 8a544285..8e93c812 100644 --- a/target/nextflow/utils/concatRuns/.config.vsh.yaml +++ b/target/nextflow/utils/concatRuns/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "concatRuns" namespace: "utils" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Arguments" arguments: @@ -160,14 +160,14 @@ build_info: output: "target/nextflow/utils/concatRuns" executable: "target/nextflow/utils/concatRuns/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" dependencies: - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -199,7 +199,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/concatRuns/_viash.yaml b/target/nextflow/utils/concatRuns/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/utils/concatRuns/_viash.yaml +++ b/target/nextflow/utils/concatRuns/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/utils/concatRuns/main.nf b/target/nextflow/utils/concatRuns/main.nf index 575a8940..72dc2ccf 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -1,4 +1,4 @@ -// concatRuns v0.9.0 +// concatRuns v0.9.1 // // 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" : "concatRuns", "namespace" : "utils", - "version" : "v0.9.0", + "version" : "v0.9.1", "argument_groups" : [ { "name" : "Arguments", @@ -3229,13 +3229,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3253,7 +3253,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/utils/concatRuns/nextflow.config b/target/nextflow/utils/concatRuns/nextflow.config index bc2b9f9c..0619da56 100644 --- a/target/nextflow/utils/concatRuns/nextflow.config +++ b/target/nextflow/utils/concatRuns/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/concatRuns' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n' } diff --git a/target/nextflow/utils/listInputDir/.config.vsh.yaml b/target/nextflow/utils/listInputDir/.config.vsh.yaml index 52f5d948..57d00c86 100644 --- a/target/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/nextflow/utils/listInputDir/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "listInputDir" namespace: "utils" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Arguments" arguments: @@ -171,12 +171,12 @@ build_info: output: "target/nextflow/utils/listInputDir" executable: "target/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -208,7 +208,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/listInputDir/_viash.yaml b/target/nextflow/utils/listInputDir/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/utils/listInputDir/_viash.yaml +++ b/target/nextflow/utils/listInputDir/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/utils/listInputDir/main.nf b/target/nextflow/utils/listInputDir/main.nf index 07529e46..c8aad710 100644 --- a/target/nextflow/utils/listInputDir/main.nf +++ b/target/nextflow/utils/listInputDir/main.nf @@ -1,4 +1,4 @@ -// listInputDir v0.9.0 +// listInputDir v0.9.1 // // 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" : "listInputDir", "namespace" : "utils", - "version" : "v0.9.0", + "version" : "v0.9.1", "argument_groups" : [ { "name" : "Arguments", @@ -3239,13 +3239,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/listInputDir", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3263,7 +3263,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3310,7 +3310,7 @@ workflow run_wf { println("Extracting information from fastq/fasta filenames") def processed_fastqs = allFastqs.collect { f -> - def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/ + def regex = ~/^(\S+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/ def validFastq = f.name ==~ regex assert validFastq: "${f} does not match the regex ${regex}" diff --git a/target/nextflow/utils/listInputDir/nextflow.config b/target/nextflow/utils/listInputDir/nextflow.config index f787ad18..f8ad80da 100644 --- a/target/nextflow/utils/listInputDir/nextflow.config +++ b/target/nextflow/utils/listInputDir/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/listInputDir' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'List the contents of a directory and parse contained fastq files' } diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml index 2e8e7689..c253a4b0 100644 --- a/target/nextflow/utils/save_params/.config.vsh.yaml +++ b/target/nextflow/utils/save_params/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "save_params" namespace: "utils" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Inputs" arguments: @@ -128,7 +128,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.9.0" + target_tag: "v0.9.1" namespace_separator: "/" setup: - type: "apt" @@ -151,12 +151,12 @@ build_info: output: "target/nextflow/utils/save_params" executable: "target/nextflow/utils/save_params/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -188,7 +188,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/save_params/_viash.yaml b/target/nextflow/utils/save_params/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/utils/save_params/_viash.yaml +++ b/target/nextflow/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/utils/save_params/main.nf b/target/nextflow/utils/save_params/main.nf index c00b3938..a15129a1 100644 --- a/target/nextflow/utils/save_params/main.nf +++ b/target/nextflow/utils/save_params/main.nf @@ -1,4 +1,4 @@ -// save_params v0.9.0 +// save_params v0.9.1 // // 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" : "save_params", "namespace" : "utils", - "version" : "v0.9.0", + "version" : "v0.9.1", "argument_groups" : [ { "name" : "Inputs", @@ -3192,7 +3192,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.9.0", + "target_tag" : "v0.9.1", "namespace_separator" : "/", "setup" : [ { @@ -3223,13 +3223,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/utils/save_params", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3247,7 +3247,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3712,7 +3712,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/utils/save_params", - "tag" : "v0.9.0" + "tag" : "v0.9.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/utils/save_params/nextflow.config b/target/nextflow/utils/save_params/nextflow.config index d3274d6b..8c2bd940 100644 --- a/target/nextflow/utils/save_params/nextflow.config +++ b/target/nextflow/utils/save_params/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/save_params' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Save parameters to a YAML file\n' } diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index e3b9a5d6..e8f548fe 100644 --- a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "htrnaseq" namespace: "workflows" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -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: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" dependencies: - "target/nextflow/stats/combine_star_logs" - "target/nextflow/stats/generate_pool_statistics" @@ -363,7 +363,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -395,7 +395,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/htrnaseq/_viash.yaml b/target/nextflow/workflows/htrnaseq/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/workflows/htrnaseq/_viash.yaml +++ b/target/nextflow/workflows/htrnaseq/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/htrnaseq/main.nf b/target/nextflow/workflows/htrnaseq/main.nf index 116f338e..e143a7fd 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -1,4 +1,4 @@ -// htrnaseq v0.9.0 +// htrnaseq v0.9.1 // // 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 @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "htrnaseq", "namespace" : "workflows", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3484,13 +3484,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3508,7 +3508,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/htrnaseq/nextflow.config b/target/nextflow/workflows/htrnaseq/nextflow.config index ea11187e..0ca0e11e 100644 --- a/target/nextflow/workflows/htrnaseq/nextflow.config +++ b/target/nextflow/workflows/htrnaseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/htrnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index ff7b60d6..6d8a1ab5 100644 --- a/target/nextflow/workflows/runner/.config.vsh.yaml +++ b/target/nextflow/workflows/runner/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "runner" namespace: "workflows" -version: "v0.9.0" +version: "v0.9.1" argument_groups: - name: "Input arguments" arguments: @@ -127,6 +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: @@ -230,9 +235,9 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" dependencies: - "target/nextflow/utils/listInputDir" - "target/nextflow/workflows/htrnaseq" @@ -241,7 +246,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -273,7 +278,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/runner/_viash.yaml b/target/nextflow/workflows/runner/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/workflows/runner/_viash.yaml +++ b/target/nextflow/workflows/runner/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/runner/main.nf b/target/nextflow/workflows/runner/main.nf index 946f4243..cd5fbdb1 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.9.0 +// runner v0.9.1 // // 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" : "runner", "namespace" : "workflows", - "version" : "v0.9.0", + "version" : "v0.9.1", "argument_groups" : [ { "name" : "Input arguments", @@ -3191,6 +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", @@ -3325,13 +3333,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3349,7 +3357,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", @@ -3399,24 +3407,6 @@ workflow run_wf { return [id, new_state] } - - // When this workflow is being used as a subworkflow, the publish directories might be defined - // in the state and not in params. The following snippets make sure the values are copied from state to params. - set_publish_dirs_channel = raw_ch - | toSortedList() - | map {ids_and_states -> - def publish_dir_arguments = ["results_publish_dir", "fastq_publish_dir"] - for (publish_dir_arg in publish_dir_arguments) { - if (!params.containsKey(publish_dir_arg)) { - def state_items = ids_and_states.collect{it[1].get(publish_dir_arg)} - assert state_items.toSet().size() == state_items.size(), "Items for '${publish_dir_arg}' must be unique! Found ${state_items}" - params[publish_dir_arg] = state_items[0] - } - } - ids_and_states - } - - save_params_ch = input_ch | toSortedList() | map { states -> @@ -3555,11 +3545,7 @@ workflow run_wf { } - // Use combine here in order to be sure tha the publish dirs are set in params - // set_publish_dirs_channel should contain 1 event; so the result of the combine - // contains the events from grouped_with_params_list_ch - results_publish_ch = grouped_with_params_list_ch.combine(set_publish_dirs_channel) - | map {event -> [event[0], event[1]]} + results_publish_ch = grouped_with_params_list_ch | publish_results.run( fromState: { id, state -> def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}" @@ -3587,7 +3573,7 @@ workflow run_wf { ] ) - fastq_publish_split_ch = grouped_ch + fastq_publish_ch = grouped_ch | flatMap{id, state -> def new_states = state.fastq_output.collect{fastq_dir -> def run_id = fastq_dir.name // The folder name corresponds to the run @@ -3603,9 +3589,6 @@ workflow run_wf { } return new_states } - - fastq_publish_ch = fastq_publish_split_ch.combine(set_publish_dirs_channel) - | map{event -> [event[0], event[1]]} | publish_fastqs.run( fromState: { id, state -> def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}" diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config index 30b126f9..88dc0a30 100644 --- a/target/nextflow/workflows/runner/nextflow.config +++ b/target/nextflow/workflows/runner/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/runner' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Runner for HT RNA-seq pipeline' } diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 746c16bc..7224370a 100644 --- a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml +++ b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_demultiplex" namespace: "workflows" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -217,15 +217,15 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.3.1/nextflow/cutadapt" - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -257,7 +257,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_demultiplex/_viash.yaml b/target/nextflow/workflows/well_demultiplex/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/workflows/well_demultiplex/_viash.yaml +++ b/target/nextflow/workflows/well_demultiplex/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/well_demultiplex/main.nf b/target/nextflow/workflows/well_demultiplex/main.nf index 3a03debc..fa28ba4b 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -1,4 +1,4 @@ -// well_demultiplex v0.9.0 +// well_demultiplex v0.9.1 // // 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 @@ -3036,7 +3036,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_demultiplex", "namespace" : "workflows", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3319,13 +3319,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3343,7 +3343,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_demultiplex/nextflow.config b/target/nextflow/workflows/well_demultiplex/nextflow.config index 774fc8be..3a358932 100644 --- a/target/nextflow/workflows/well_demultiplex/nextflow.config +++ b/target/nextflow/workflows/well_demultiplex/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_demultiplex' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' description = 'Demultiplexing on well level' author = 'Dries Schaumont, Marijke Van Moerbeke' } diff --git a/target/nextflow/workflows/well_metadata/.config.vsh.yaml b/target/nextflow/workflows/well_metadata/.config.vsh.yaml index c49db106..ecf80f96 100644 --- a/target/nextflow/workflows/well_metadata/.config.vsh.yaml +++ b/target/nextflow/workflows/well_metadata/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_metadata" namespace: "workflows" -version: "v0.9.0" +version: "v0.9.1" authors: - name: "Dries Schaumont" roles: @@ -215,12 +215,12 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.4" - git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a" + git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22" git_remote: "https://github.com/viash-hub/htrnaseq" - git_tag: "v0.7.2-11-g8afa5dc" + git_tag: "v0.9.0-3-g1bce00e" package_config: name: "htrnaseq" - version: "v0.9.0" + version: "v0.9.1" summary: "A workflow for high-throughput RNA-seq data analyses.\n" description: "This workflow is designed to process high-throughput RNA-seq data,\ \ where every\nwell of a microarray plate is a sample. A fasta file provided as\ @@ -252,7 +252,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.9.1'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_metadata/_viash.yaml b/target/nextflow/workflows/well_metadata/_viash.yaml index 0b594cc5..c00e2cb1 100644 --- a/target/nextflow/workflows/well_metadata/_viash.yaml +++ b/target/nextflow/workflows/well_metadata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.9.0 +version: v0.9.1 summary: | A workflow for high-throughput RNA-seq data analyses. description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n" diff --git a/target/nextflow/workflows/well_metadata/main.nf b/target/nextflow/workflows/well_metadata/main.nf index 3344bc1b..17bb6a39 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -1,4 +1,4 @@ -// well_metadata v0.9.0 +// well_metadata v0.9.1 // // 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 @@ -3035,7 +3035,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "well_metadata", "namespace" : "workflows", - "version" : "v0.9.0", + "version" : "v0.9.1", "authors" : [ { "name" : "Dries Schaumont", @@ -3299,13 +3299,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.4", - "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a", + "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22", "git_remote" : "https://github.com/viash-hub/htrnaseq", - "git_tag" : "v0.7.2-11-g8afa5dc" + "git_tag" : "v0.9.0-3-g1bce00e" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.9.0", + "version" : "v0.9.1", "summary" : "A workflow for high-throughput RNA-seq data analyses.\n", "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n", "info" : { @@ -3323,7 +3323,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.9.0'" + ".engines[.type == 'docker'].target_tag := 'v0.9.1'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_metadata/nextflow.config b/target/nextflow/workflows/well_metadata/nextflow.config index 50bbf278..cc53ebe3 100644 --- a/target/nextflow/workflows/well_metadata/nextflow.config +++ b/target/nextflow/workflows/well_metadata/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_metadata' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.9.0' + version = 'v0.9.1' author = 'Dries Schaumont' }