From 44dc2ea48d340d1e259c6d902012ab15283b5a07 Mon Sep 17 00:00:00 2001 From: CI Date: Mon, 23 Feb 2026 14:33:34 +0000 Subject: [PATCH] Build branch htrnaseq/v0.14 with version v0.14.6 to htrnaseq on branch v0.14 (9346c55) Build pipeline: viash-hub.htrnaseq.v0.14.6-q286w Source commit: https://github.com/viash-hub/htrnaseq/commit/9346c55e3f894994935b0928759dca9e56866d37 Source message: Bump version to v0.14.6 --- CHANGELOG.md | 6 ++ _viash.yaml | 2 +- src/utils/save_params/config.vsh.yaml | 7 ++- src/utils/save_params/script.py | 31 +++++++++- src/workflows/runner/main.nf | 40 ++++++++++-- .../utils/listInputDir/.config.vsh.yaml | 8 +-- .../nextflow/utils/listInputDir/_viash.yaml | 2 +- .../nextflow/utils/listInputDir/main.nf | 10 +-- .../utils/listInputDir/nextflow.config | 2 +- .../well_fastqs_to_esets/.config.vsh.yaml | 8 +-- .../well_fastqs_to_esets/_viash.yaml | 2 +- .../workflows/well_fastqs_to_esets/main.nf | 10 +-- .../well_fastqs_to_esets/nextflow.config | 2 +- .../eset/create_eset/.config.vsh.yaml | 10 +-- .../executable/eset/create_eset/_viash.yaml | 2 +- .../executable/eset/create_eset/create_eset | 14 ++--- .../eset/create_fdata/.config.vsh.yaml | 10 +-- .../executable/eset/create_fdata/_viash.yaml | 2 +- .../executable/eset/create_fdata/create_fdata | 14 ++--- .../eset/create_pdata/.config.vsh.yaml | 10 +-- .../executable/eset/create_pdata/_viash.yaml | 2 +- .../executable/eset/create_pdata/create_pdata | 14 ++--- .../htrnaseq/check_eset/.config.vsh.yaml | 10 +-- .../htrnaseq/check_eset/_viash.yaml | 2 +- .../htrnaseq/check_eset/check_eset | 14 ++--- .../check_cutadapt_output/.config.vsh.yaml | 10 +-- .../check_cutadapt_output/_viash.yaml | 2 +- .../check_cutadapt_output | 14 ++--- .../io/publish_fastqs/.config.vsh.yaml | 10 +-- .../executable/io/publish_fastqs/_viash.yaml | 2 +- .../io/publish_fastqs/publish_fastqs | 14 ++--- .../io/publish_results/.config.vsh.yaml | 10 +-- .../executable/io/publish_results/_viash.yaml | 2 +- .../io/publish_results/publish_results | 14 ++--- .../executable/parallel_map/.config.vsh.yaml | 10 +-- target/executable/parallel_map/_viash.yaml | 2 +- target/executable/parallel_map/parallel_map | 14 ++--- .../report/create_report/.config.vsh.yaml | 10 +-- .../report/create_report/_viash.yaml | 2 +- .../report/create_report/create_report | 14 ++--- .../stats/combine_star_logs/.config.vsh.yaml | 10 +-- .../stats/combine_star_logs/_viash.yaml | 2 +- .../stats/combine_star_logs/combine_star_logs | 14 ++--- .../generate_pool_statistics/.config.vsh.yaml | 10 +-- .../generate_pool_statistics/_viash.yaml | 2 +- .../generate_pool_statistics | 14 ++--- .../generate_well_statistics/.config.vsh.yaml | 10 +-- .../generate_well_statistics/_viash.yaml | 2 +- .../generate_well_statistics | 14 ++--- .../utils/save_params/.config.vsh.yaml | 23 ++++--- .../executable/utils/save_params/_viash.yaml | 2 +- .../executable/utils/save_params/save_params | 61 ++++++++++++++++--- .../eset/create_eset/.config.vsh.yaml | 10 +-- target/nextflow/eset/create_eset/_viash.yaml | 2 +- target/nextflow/eset/create_eset/main.nf | 14 ++--- .../nextflow/eset/create_eset/nextflow.config | 2 +- .../eset/create_fdata/.config.vsh.yaml | 10 +-- target/nextflow/eset/create_fdata/_viash.yaml | 2 +- target/nextflow/eset/create_fdata/main.nf | 14 ++--- .../eset/create_fdata/nextflow.config | 2 +- .../eset/create_pdata/.config.vsh.yaml | 10 +-- target/nextflow/eset/create_pdata/_viash.yaml | 2 +- target/nextflow/eset/create_pdata/main.nf | 14 ++--- .../eset/create_pdata/nextflow.config | 2 +- .../htrnaseq/check_eset/.config.vsh.yaml | 10 +-- .../htrnaseq/check_eset/_viash.yaml | 2 +- .../htrnaseq/check_eset/main.nf | 14 ++--- .../htrnaseq/check_eset/nextflow.config | 2 +- .../check_cutadapt_output/.config.vsh.yaml | 10 +-- .../check_cutadapt_output/_viash.yaml | 2 +- .../check_cutadapt_output/main.nf | 14 ++--- .../check_cutadapt_output/nextflow.config | 2 +- .../io/publish_fastqs/.config.vsh.yaml | 10 +-- target/nextflow/io/publish_fastqs/_viash.yaml | 2 +- target/nextflow/io/publish_fastqs/main.nf | 14 ++--- .../io/publish_fastqs/nextflow.config | 2 +- .../io/publish_results/.config.vsh.yaml | 10 +-- .../nextflow/io/publish_results/_viash.yaml | 2 +- target/nextflow/io/publish_results/main.nf | 14 ++--- .../io/publish_results/nextflow.config | 2 +- target/nextflow/parallel_map/.config.vsh.yaml | 10 +-- target/nextflow/parallel_map/_viash.yaml | 2 +- target/nextflow/parallel_map/main.nf | 14 ++--- target/nextflow/parallel_map/nextflow.config | 2 +- .../report/create_report/.config.vsh.yaml | 10 +-- .../nextflow/report/create_report/_viash.yaml | 2 +- target/nextflow/report/create_report/main.nf | 14 ++--- .../report/create_report/nextflow.config | 2 +- .../stats/combine_star_logs/.config.vsh.yaml | 10 +-- .../stats/combine_star_logs/_viash.yaml | 2 +- .../nextflow/stats/combine_star_logs/main.nf | 14 ++--- .../stats/combine_star_logs/nextflow.config | 2 +- .../generate_pool_statistics/.config.vsh.yaml | 10 +-- .../generate_pool_statistics/_viash.yaml | 2 +- .../stats/generate_pool_statistics/main.nf | 14 ++--- .../generate_pool_statistics/nextflow.config | 2 +- .../generate_well_statistics/.config.vsh.yaml | 10 +-- .../generate_well_statistics/_viash.yaml | 2 +- .../stats/generate_well_statistics/main.nf | 14 ++--- .../generate_well_statistics/nextflow.config | 2 +- .../utils/concatRuns/.config.vsh.yaml | 8 +-- target/nextflow/utils/concatRuns/_viash.yaml | 2 +- target/nextflow/utils/concatRuns/main.nf | 10 +-- .../nextflow/utils/concatRuns/nextflow.config | 2 +- .../utils/save_params/.config.vsh.yaml | 23 ++++--- target/nextflow/utils/save_params/_viash.yaml | 2 +- target/nextflow/utils/save_params/main.nf | 56 ++++++++++++++--- .../utils/save_params/nextflow.config | 2 +- .../utils/save_params/nextflow_schema.json | 9 ++- .../workflows/htrnaseq/.config.vsh.yaml | 8 +-- .../nextflow/workflows/htrnaseq/_viash.yaml | 2 +- target/nextflow/workflows/htrnaseq/main.nf | 10 +-- .../workflows/htrnaseq/nextflow.config | 2 +- .../workflows/runner/.config.vsh.yaml | 8 +-- target/nextflow/workflows/runner/_viash.yaml | 2 +- target/nextflow/workflows/runner/main.nf | 50 ++++++++++++--- .../nextflow/workflows/runner/nextflow.config | 2 +- .../well_demultiplex/.config.vsh.yaml | 8 +-- .../workflows/well_demultiplex/_viash.yaml | 2 +- .../workflows/well_demultiplex/main.nf | 10 +-- .../well_demultiplex/nextflow.config | 2 +- .../workflows/well_metadata/.config.vsh.yaml | 8 +-- .../workflows/well_metadata/_viash.yaml | 2 +- .../nextflow/workflows/well_metadata/main.nf | 10 +-- .../workflows/well_metadata/nextflow.config | 2 +- 125 files changed, 653 insertions(+), 453 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f916bffe..f9c1b693 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# htrnaseq v0.14.6 + +## Minor changes + +* Update `utils/save_params` to capture sub-workflow names and versions alongside input parameters (PR #95). + # htrnaseq v0.14.5 ## Bug fixes diff --git a/_viash.yaml b/_viash.yaml index ba1471d3..7758cabb 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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/src/utils/save_params/config.vsh.yaml b/src/utils/save_params/config.vsh.yaml index d21924da..0739ce75 100644 --- a/src/utils/save_params/config.vsh.yaml +++ b/src/utils/save_params/config.vsh.yaml @@ -16,6 +16,11 @@ argument_groups: base64 encoded yaml containing the state type: string required: true + - name: "--workflow_analysis" + description: | + Base64 encoded YAML containing workflow analysis information (name and version for all workflows) + type: string + required: false - name: Outputs arguments: @@ -23,9 +28,9 @@ argument_groups: description: | The output YAML file type: file + default: "params.yaml" direction: output required: true - example: "output.yaml" resources: - type: python_script diff --git a/src/utils/save_params/script.py b/src/utils/save_params/script.py index 0eed41d9..2eeec623 100644 --- a/src/utils/save_params/script.py +++ b/src/utils/save_params/script.py @@ -6,14 +6,23 @@ import base64 par = { "id": "sample_one", "params_yaml": "cGFyYW1zX3lhbWw6IHt9Cg==", + "workflow_analysis": "LSBuYW1lOiBhbm5vdFZpc1FDX3dmCiAgdmVyc2lvbjogMC4xLjAK", "output": "output.yaml" } ## VIASH END +# Custom representer to preserve dict order in YAML output +# Note: Python 3.7+ dicts maintain insertion order by default +def represent_dict(dumper, data): + return dumper.represent_dict(data.items()) + class Dumper(yaml.Dumper): def increase_indent(self, flow=False, indentless=False): return super(Dumper, self).increase_indent(flow, False) +# Register the representer for dicts to preserve order +Dumper.add_representer(dict, represent_dict) + def decode_params_yaml(encoded_yaml): yaml_bytes = base64.b64decode(encoded_yaml) yaml_string = yaml_bytes.decode('utf-8') @@ -23,6 +32,24 @@ def decode_params_yaml(encoded_yaml): params = decode_params_yaml(par['params_yaml']) -with open(par["output"], 'w') as f: - yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) +# Build the output structure +output_data = params # params is a list of states + +# Add workflow analysis information if provided +if par.get('workflow_analysis'): + try: + analysis_bytes = base64.b64decode(par['workflow_analysis']) + analysis_string = analysis_bytes.decode('utf-8') + analysis = yaml.safe_load(analysis_string) + # Since params is a list, create a dict wrapper + output_data = { + 'params': params, + 'analysis': analysis + } + except (TypeError, ValueError) as e: + e.add_note("Could not parse workflow_analysis YAML.") + raise + +with open(par["output"], 'w') as f: + yaml.dump(output_data, f, default_flow_style=False, Dumper=Dumper) diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index 65608f4e..7796c2c5 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -6,8 +6,6 @@ def date = new Date().format('yyyyMMdd_hhmmss') session = nextflow.Nextflow.getSession() final service = session.publishDirExecutorService() - - def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml") def version = get_version(viash_config) @@ -21,6 +19,33 @@ def regex_trailing_slashes = ~/\/+$/ def results_publish_dir = params.results_publish_dir - regex_trailing_slashes def fastq_publish_dir = params.fastq_publish_dir - regex_trailing_slashes +def get_workflow_analysis() { + def dependencies = [] + + if (meta.config.dependencies) { + meta.config.dependencies.each { dep_spec -> + def dependency_name = dep_spec.alias ? dep_spec.alias : dep_spec.name + def dependency_var = file(dependency_name).name + def dependency = binding.getVariable(dependency_var) + + def dep_entry = new LinkedHashMap() + dep_entry.name = dependency.config.name ?: "unknown_name" + dep_entry.version = dependency.config.version ?: "unknown_version" + dependencies << dep_entry + } + } + + // Build main analysis entry with dependencies using LinkedHashMap for order + def main_entry = new LinkedHashMap() + main_entry.name = meta.config.name ?: "unknown_name" + main_entry.version = meta.config.version ?: "unknown_version" + main_entry.dependencies = dependencies + + def analysis = [main_entry] + + println("Analysis workflows: ${analysis}") + return analysis +} /* This is a utility workflow that gathers the input events and saves their state to a YAML file. @@ -44,7 +69,6 @@ workflow save_params_wf { | save_params.run( key: "save_params_runner", fromState: {id, state -> - def convertPaths convertPaths = { value -> if (value instanceof java.nio.file.Path) @@ -64,13 +88,19 @@ workflow save_params_wf { def yamlString = yaml.dump(convertedState) def encodedYaml = yamlString.bytes.encodeBase64().toString() + def yaml_builder = new org.yaml.snakeyaml.Yaml() + def analysis_yaml = yaml_builder.dump(get_workflow_analysis()) + def encoded_analysis = analysis_yaml.bytes.encodeBase64().toString() + return [ "id": id, "params_yaml": encodedYaml, - "output": state.run_params + "workflow_analysis": encoded_analysis ] }, - toState: ["run_params": "output"] + toState: { id, output, state -> + state + [ run_params: output.output ] + } ) emit: diff --git a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml index 5af3bccb..d7a2c4c2 100644 --- a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml +++ b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "listInputDir" namespace: "utils" -version: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Arguments" arguments: @@ -169,11 +169,11 @@ build_info: output: "target/_private/nextflow/utils/listInputDir" executable: "target/_private/nextflow/utils/listInputDir/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -205,7 +205,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/_private/nextflow/utils/listInputDir/_viash.yaml b/target/_private/nextflow/utils/listInputDir/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/_private/nextflow/utils/listInputDir/_viash.yaml +++ b/target/_private/nextflow/utils/listInputDir/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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/_private/nextflow/utils/listInputDir/main.nf b/target/_private/nextflow/utils/listInputDir/main.nf index 2171830c..0f65798f 100644 --- a/target/_private/nextflow/utils/listInputDir/main.nf +++ b/target/_private/nextflow/utils/listInputDir/main.nf @@ -1,4 +1,4 @@ -// listInputDir v0.14.5 +// listInputDir v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "argument_groups" : [ { "name" : "Arguments", @@ -3236,12 +3236,12 @@ meta = [ "engine" : "native|native", "output" : "target/_private/nextflow/utils/listInputDir", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3259,7 +3259,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/_private/nextflow/utils/listInputDir/nextflow.config b/target/_private/nextflow/utils/listInputDir/nextflow.config index 5e827361..83b27cf1 100644 --- a/target/_private/nextflow/utils/listInputDir/nextflow.config +++ b/target/_private/nextflow/utils/listInputDir/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'utils/listInputDir' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.5' + version = 'v0.14.6' description = 'List the contents of a directory and parse contained fastq files' } diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml b/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml index f00b9c67..d67c3b92 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "well_fastqs_to_esets" namespace: "workflows" -version: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -323,7 +323,7 @@ build_info: output: "target/_private/nextflow/workflows/well_fastqs_to_esets" executable: "target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/stats/combine_star_logs" @@ -340,7 +340,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -372,7 +372,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml b/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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/_private/nextflow/workflows/well_fastqs_to_esets/main.nf b/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf index 78a1d41c..300af4e6 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/main.nf @@ -1,4 +1,4 @@ -// well_fastqs_to_esets v0.14.5 +// well_fastqs_to_esets v0.14.6 // // 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_fastqs_to_esets", "namespace" : "workflows", - "version" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3455,12 +3455,12 @@ meta = [ "engine" : "native|native", "output" : "target/_private/nextflow/workflows/well_fastqs_to_esets", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3478,7 +3478,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config b/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config index 08e39684..0c3e216e 100644 --- a/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config +++ b/target/_private/nextflow/workflows/well_fastqs_to_esets/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/well_fastqs_to_esets' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.5' + version = 'v0.14.6' description = 'Map a list of FASTQ files (one for each well) to a reference genome and generate count matrices.\nSometimes counts from different FASTQ files need to be concatenated. This is done bases on the sample_id:\nif the sample ID of the two plates are identical, the FASTQ files will we joined _before_ mapping.\n' author = 'Dries Schaumont' } diff --git a/target/executable/eset/create_eset/.config.vsh.yaml b/target/executable/eset/create_eset/.config.vsh.yaml index fc01118d..e5d55a94 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "r" @@ -206,11 +206,11 @@ build_info: output: "target/executable/eset/create_eset" executable: "target/executable/eset/create_eset/create_eset" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -242,7 +242,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_eset/_viash.yaml b/target/executable/eset/create_eset/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/eset/create_eset/_viash.yaml +++ b/target/executable/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 22942979..3b02753f 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 v0.14.5 +# create_eset v0.14.6 # # 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="2025-12-12T15:31:35Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_eset v0.14.5" + echo "create_eset v0.14.6" echo "" echo "Arguments:" echo " --pDataFile" @@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_eset v0.14.5" + echo "create_eset v0.14.6" exit ;; --pDataFile) @@ -794,7 +794,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.6' fi # print dockerfile diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index 5e56334f..b8a0597f 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -183,11 +183,11 @@ build_info: output: "target/executable/eset/create_fdata" executable: "target/executable/eset/create_fdata/create_fdata" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -219,7 +219,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_fdata/_viash.yaml b/target/executable/eset/create_fdata/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/eset/create_fdata/_viash.yaml +++ b/target/executable/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 88f074f0..fd1f88f3 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 v0.14.5 +# create_fdata v0.14.6 # # 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="2025-12-12T15:31:35Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_fdata v0.14.5" + echo "create_fdata v0.14.6" echo "" echo "Create a fdata file" echo "" @@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_fdata v0.14.5" + echo "create_fdata v0.14.6" exit ;; --gtf) @@ -756,7 +756,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.6' fi # print dockerfile diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index 7cc3ed11..a3538e27 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -197,11 +197,11 @@ build_info: output: "target/executable/eset/create_pdata" executable: "target/executable/eset/create_pdata/create_pdata" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -233,7 +233,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_pdata/_viash.yaml b/target/executable/eset/create_pdata/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/eset/create_pdata/_viash.yaml +++ b/target/executable/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 13f2134d..8b53cfa0 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 v0.14.5 +# create_pdata v0.14.6 # # 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="2025-12-12T15:31:35Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pdata v0.14.5" + echo "create_pdata v0.14.6" echo "" echo "Create a pdata file by combining the mapping statistics" echo "" @@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pdata v0.14.5" + echo "create_pdata v0.14.6" exit ;; --star_stats_file) @@ -777,7 +777,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.6' 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 786af87c..d4773c19 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "r" @@ -155,11 +155,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -191,7 +191,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" 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 ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 19070a86..80b84b1e 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 v0.14.5 +# check_eset v0.14.6 # # 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="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_eset v0.14.5" + echo "check_eset v0.14.6" echo "" echo "This component test the ExpressionSet object as output by the main pipeline." echo "" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_eset v0.14.5" + echo "check_eset v0.14.6" exit ;; --eset) @@ -754,7 +754,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.6' 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 67a86185..20dc61d5 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -164,11 +164,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -200,7 +200,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" 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 ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 3c08ca1d..ceed99f0 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 v0.14.5 +# check_cutadapt_output v0.14.6 # # 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="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" 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 v0.14.5" + echo "check_cutadapt_output v0.14.6" echo "" echo "This component test the cutadapt output from the well_demultiplex subworkflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_cutadapt_output v0.14.5" + echo "check_cutadapt_output v0.14.6" exit ;; --fastq_r1) @@ -783,7 +783,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.6' fi # print dockerfile diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 09092a6c..2891b7e7 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -139,11 +139,11 @@ build_info: output: "target/executable/io/publish_fastqs" executable: "target/executable/io/publish_fastqs/publish_fastqs" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -175,7 +175,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_fastqs/_viash.yaml b/target/executable/io/publish_fastqs/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/io/publish_fastqs/_viash.yaml +++ b/target/executable/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 c7d69dda..3a429dc2 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 v0.14.5 +# publish_fastqs v0.14.6 # # 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="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:12Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_fastqs v0.14.5" + echo "publish_fastqs v0.14.6" echo "" echo "Publish the fastq files per well" echo "" @@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_fastqs v0.14.5" + echo "publish_fastqs v0.14.6" exit ;; --input) @@ -750,7 +750,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.6' fi # print dockerfile diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index 82083ac0..ca918ed1 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: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Input arguments" arguments: @@ -261,7 +261,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -315,7 +315,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_results/_viash.yaml b/target/executable/io/publish_results/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/io/publish_results/_viash.yaml +++ b/target/executable/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 35d29bfd..9bf6d780 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 v0.14.5 +# publish_results v0.14.6 # # 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="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:12Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_results v0.14.5" + echo "publish_results v0.14.6" echo "" echo "Publish the results" echo "" @@ -683,7 +683,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_results v0.14.5" + echo "publish_results v0.14.6" exit ;; --star_output) @@ -986,7 +986,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.6' fi # print dockerfile diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 4e8868da..227987ee 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -285,11 +285,11 @@ build_info: output: "target/executable/parallel_map" executable: "target/executable/parallel_map/parallel_map" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -321,7 +321,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/parallel_map/_viash.yaml b/target/executable/parallel_map/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/parallel_map/_viash.yaml +++ b/target/executable/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 a069a599..6ad312cb 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 v0.14.5 +# parallel_map v0.14.6 # # 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="2025-12-12T15:31:37Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:11Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "parallel_map v0.14.5" + echo "parallel_map v0.14.6" echo "" echo "Map wells in batch, using STAR" echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin" @@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "parallel_map v0.14.5" + echo "parallel_map v0.14.6" exit ;; --input_r1) @@ -907,7 +907,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.6' fi # print dockerfile diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index c1dc2bf2..467f06e1 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -168,7 +168,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -225,11 +225,11 @@ build_info: output: "target/executable/report/create_report" executable: "target/executable/report/create_report/create_report" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -261,7 +261,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/report/create_report/_viash.yaml b/target/executable/report/create_report/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/report/create_report/_viash.yaml +++ b/target/executable/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 5a1fb30d..d5e51654 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 v0.14.5 +# create_report v0.14.6 # # 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="2025-12-12T15:31:34Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_report v0.14.5" + echo "create_report v0.14.6" echo "" echo "Create a basic QC report in HTML format based on a number of esets." echo "" @@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_report v0.14.5" + echo "create_report v0.14.6" exit ;; --eset) @@ -777,7 +777,7 @@ if [[ "$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/report/create_report:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.6' 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 3a6c980d..ef460bed 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -204,11 +204,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -240,7 +240,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/combine_star_logs/_viash.yaml b/target/executable/stats/combine_star_logs/_viash.yaml index ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 d4a0634a..92fa8372 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 v0.14.5 +# combine_star_logs v0.14.6 # # 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="2025-12-12T15:31:34Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" 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 v0.14.5" + echo "combine_star_logs v0.14.6" echo "" echo "Arguments:" echo " --barcodes" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "combine_star_logs v0.14.5" + echo "combine_star_logs v0.14.6" exit ;; --barcodes) @@ -825,7 +825,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.6' 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 61232d80..fb393839 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -188,11 +188,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -224,7 +224,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_pool_statistics/_viash.yaml b/target/executable/stats/generate_pool_statistics/_viash.yaml index ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 d163ae6b..a810a034 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 v0.14.5 +# generate_pool_statistics v0.14.6 # # 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="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" 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 v0.14.5" + echo "generate_pool_statistics v0.14.6" echo "" echo "Arguments:" echo " --nrReadsNrGenesPerChrom" @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_pool_statistics v0.14.5" + echo "generate_pool_statistics v0.14.6" exit ;; --nrReadsNrGenesPerChrom) @@ -767,7 +767,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.6' 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 db17b19d..d841de03 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -230,7 +230,7 @@ engines: id: "docker" image: "python:3.13-trixie" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -260,11 +260,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -296,7 +296,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_well_statistics/_viash.yaml b/target/executable/stats/generate_well_statistics/_viash.yaml index ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 01c70260..348895fb 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 v0.14.5 +# generate_well_statistics v0.14.6 # # 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_well_statistics" -LABEL org.opencontainers.image.created="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "generate_well_statistics v0.14.5" + echo "generate_well_statistics v0.14.6" echo "" echo "Generate summary statistics from BAM files generated by STAR solo." echo "" @@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_well_statistics v0.14.5" + echo "generate_well_statistics v0.14.6" exit ;; --input) @@ -861,7 +861,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.6' fi # print dockerfile diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml index 5ef3d02c..eae8243c 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: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Inputs" arguments: @@ -20,14 +20,23 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "string" + name: "--workflow_analysis" + description: "Base64 encoded YAML containing workflow analysis information (name\ + \ and version for all workflows)\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" - name: "Outputs" arguments: - type: "file" name: "--output" description: "The output YAML file\n" info: null - example: - - "output.yaml" + default: + - "params.yaml" must_exist: true create_parent: true required: true @@ -128,7 +137,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -151,11 +160,11 @@ build_info: output: "target/executable/utils/save_params" executable: "target/executable/utils/save_params/save_params" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -187,7 +196,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/utils/save_params/_viash.yaml b/target/executable/utils/save_params/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/executable/utils/save_params/_viash.yaml +++ b/target/executable/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 081bbf84..704f05f5 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 v0.14.5 +# save_params v0.14.6 # # 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="2025-12-12T15:31:36Z" +LABEL org.opencontainers.image.created="2026-02-23T13:37:10Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9d5018b257513e527f13faf524f1e9e6df01c465" -LABEL org.opencontainers.image.version="v0.14.5" +LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" +LABEL org.opencontainers.image.version="v0.14.6" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "save_params v0.14.5" + echo "save_params v0.14.6" echo "" echo "Save parameters to a YAML file" echo "" @@ -586,10 +586,15 @@ function ViashHelp { echo " type: string, required parameter" echo " base64 encoded yaml containing the state" echo "" + echo " --workflow_analysis" + echo " type: string" + echo " Base64 encoded YAML containing workflow analysis information (name and" + echo " version for all workflows)" + echo "" echo "Outputs:" echo " --output" echo " type: file, required parameter, output, file must exist" - echo " example: output.yaml" + echo " default: params.yaml" echo " The output YAML file" echo "" echo "Viash built in Computational Requirements:" @@ -639,7 +644,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "save_params v0.14.5" + echo "save_params v0.14.6" exit ;; --id) @@ -664,6 +669,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_PARAMS_YAML=$(ViashRemoveFlags "$1") shift 1 ;; + --workflow_analysis) + [ -n "$VIASH_PAR_WORKFLOW_ANALYSIS" ] && ViashError Bad arguments for option \'--workflow_analysis\': \'$VIASH_PAR_WORKFLOW_ANALYSIS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WORKFLOW_ANALYSIS="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --workflow_analysis. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --workflow_analysis=*) + [ -n "$VIASH_PAR_WORKFLOW_ANALYSIS" ] && ViashError Bad arguments for option \'--workflow_analysis=*\': \'$VIASH_PAR_WORKFLOW_ANALYSIS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_WORKFLOW_ANALYSIS=$(ViashRemoveFlags "$1") + shift 1 + ;; --output) [ -n "$VIASH_PAR_OUTPUT" ] && ViashError Bad arguments for option \'--output\': \'$VIASH_PAR_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_OUTPUT="$2" @@ -763,7 +779,7 @@ if [[ "$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:v0.14.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.6' fi # print dockerfile @@ -1056,6 +1072,7 @@ import base64 par = { 'id': $( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "r'${VIASH_PAR_ID//\'/\'\"\'\"r\'}'"; else echo None; fi ), 'params_yaml': $( if [ ! -z ${VIASH_PAR_PARAMS_YAML+x} ]; then echo "r'${VIASH_PAR_PARAMS_YAML//\'/\'\"\'\"r\'}'"; else echo None; fi ), + 'workflow_analysis': $( if [ ! -z ${VIASH_PAR_WORKFLOW_ANALYSIS+x} ]; then echo "r'${VIASH_PAR_WORKFLOW_ANALYSIS//\'/\'\"\'\"r\'}'"; else echo None; fi ), 'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\'/\'\"\'\"r\'}'"; else echo None; fi ) } meta = { @@ -1084,10 +1101,18 @@ dep = { ## VIASH END +# Custom representer to preserve dict order in YAML output +# Note: Python 3.7+ dicts maintain insertion order by default +def represent_dict(dumper, data): + return dumper.represent_dict(data.items()) + class Dumper(yaml.Dumper): def increase_indent(self, flow=False, indentless=False): return super(Dumper, self).increase_indent(flow, False) +# Register the representer for dicts to preserve order +Dumper.add_representer(dict, represent_dict) + def decode_params_yaml(encoded_yaml): yaml_bytes = base64.b64decode(encoded_yaml) yaml_string = yaml_bytes.decode('utf-8') @@ -1097,8 +1122,26 @@ def decode_params_yaml(encoded_yaml): params = decode_params_yaml(par['params_yaml']) +# Build the output structure +output_data = params # params is a list of states + +# Add workflow analysis information if provided +if par.get('workflow_analysis'): + try: + analysis_bytes = base64.b64decode(par['workflow_analysis']) + analysis_string = analysis_bytes.decode('utf-8') + analysis = yaml.safe_load(analysis_string) + # Since params is a list, create a dict wrapper + output_data = { + 'params': params, + 'analysis': analysis + } + except (TypeError, ValueError) as e: + e.add_note("Could not parse workflow_analysis YAML.") + raise + with open(par["output"], 'w') as f: - yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) + yaml.dump(output_data, f, default_flow_style=False, Dumper=Dumper) VIASHMAIN python -B "\$tempscript" & wait "\$!" diff --git a/target/nextflow/eset/create_eset/.config.vsh.yaml b/target/nextflow/eset/create_eset/.config.vsh.yaml index 2fa8a6cc..99521e46 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "r" @@ -206,11 +206,11 @@ build_info: output: "target/nextflow/eset/create_eset" executable: "target/nextflow/eset/create_eset/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -242,7 +242,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_eset/_viash.yaml b/target/nextflow/eset/create_eset/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/eset/create_eset/_viash.yaml +++ b/target/nextflow/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 8ea5f7c1..c143516c 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -1,4 +1,4 @@ -// create_eset v0.14.5 +// create_eset v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3271,7 +3271,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3309,12 +3309,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3332,7 +3332,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -4217,7 +4217,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_eset", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_eset/nextflow.config b/target/nextflow/eset/create_eset/nextflow.config index df81adb1..3c9fb93d 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 = 'v0.14.5' + version = 'v0.14.6' 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 ce04e8f3..25c9dac0 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -183,11 +183,11 @@ build_info: output: "target/nextflow/eset/create_fdata" executable: "target/nextflow/eset/create_fdata/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -219,7 +219,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_fdata/_viash.yaml b/target/nextflow/eset/create_fdata/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/eset/create_fdata/_viash.yaml +++ b/target/nextflow/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 cbfc2261..9bbffc2c 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -1,4 +1,4 @@ -// create_fdata v0.14.5 +// create_fdata v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3279,12 +3279,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3302,7 +3302,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3872,7 +3872,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_fdata", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_fdata/nextflow.config b/target/nextflow/eset/create_fdata/nextflow.config index 686d9648..81620665 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 = 'v0.14.5' + version = 'v0.14.6' 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 edea824b..ac7b411a 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -197,11 +197,11 @@ build_info: output: "target/nextflow/eset/create_pdata" executable: "target/nextflow/eset/create_pdata/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -233,7 +233,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_pdata/_viash.yaml b/target/nextflow/eset/create_pdata/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/eset/create_pdata/_viash.yaml +++ b/target/nextflow/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 24bd8e41..c8abe63e 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -1,4 +1,4 @@ -// create_pdata v0.14.5 +// create_pdata v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3252,7 +3252,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3293,12 +3293,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3316,7 +3316,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3812,7 +3812,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_pdata", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_pdata/nextflow.config b/target/nextflow/eset/create_pdata/nextflow.config index 869364d4..f3a333e5 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 = 'v0.14.5' + version = 'v0.14.6' 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 5f94b655..44167746 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "r" @@ -155,11 +155,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -191,7 +191,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" 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 ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 2f77219c..ed2d246d 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 v0.14.5 +// check_eset v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "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" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3233,12 +3233,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3256,7 +3256,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3906,7 +3906,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "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 6c303688..f9c618fa 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 = 'v0.14.5' + version = 'v0.14.6' 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 20d2b58a..a3595809 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -164,11 +164,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -200,7 +200,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" 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 ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 d2cc5cda..09e2459c 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 v0.14.5 +// check_cutadapt_output v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3213,7 +3213,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3244,12 +3244,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3267,7 +3267,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3786,7 +3786,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "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 96328eff..f85c7177 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 = 'v0.14.5' + version = 'v0.14.6' 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 299fc6e1..7fb8276d 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -139,11 +139,11 @@ build_info: output: "target/nextflow/io/publish_fastqs" executable: "target/nextflow/io/publish_fastqs/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -175,7 +175,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_fastqs/_viash.yaml b/target/nextflow/io/publish_fastqs/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/io/publish_fastqs/_viash.yaml +++ b/target/nextflow/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 1733aac3..aa6f08b5 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -1,4 +1,4 @@ -// publish_fastqs v0.14.5 +// publish_fastqs v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3184,7 +3184,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3207,12 +3207,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3230,7 +3230,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3682,7 +3682,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_fastqs", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_fastqs/nextflow.config b/target/nextflow/io/publish_fastqs/nextflow.config index c36a5ead..336b5622 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 = 'v0.14.5' + version = 'v0.14.6' 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 bd38a9f5..8081408c 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: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Input arguments" arguments: @@ -261,7 +261,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +279,11 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -315,7 +315,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_results/_viash.yaml b/target/nextflow/io/publish_results/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/io/publish_results/_viash.yaml +++ b/target/nextflow/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 a829564f..42539cf4 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -1,4 +1,4 @@ -// publish_results v0.14.5 +// publish_results v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3346,7 +3346,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3369,12 +3369,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3392,7 +3392,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3909,7 +3909,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_results", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_results/nextflow.config b/target/nextflow/io/publish_results/nextflow.config index cafdaefd..4e2cf4a1 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 = 'v0.14.5' + version = 'v0.14.6' description = 'Publish the results' } diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 09956c13..84489db3 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -285,11 +285,11 @@ build_info: output: "target/nextflow/parallel_map" executable: "target/nextflow/parallel_map/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -321,7 +321,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/parallel_map/_viash.yaml b/target/nextflow/parallel_map/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/parallel_map/_viash.yaml +++ b/target/nextflow/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 f3c59c39..5bd1bba9 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -1,4 +1,4 @@ -// parallel_map v0.14.5 +// parallel_map v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3332,7 +3332,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3379,12 +3379,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3402,7 +3402,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -4173,7 +4173,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/parallel_map", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/parallel_map/nextflow.config b/target/nextflow/parallel_map/nextflow.config index 68b80a02..33c405fd 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 = 'v0.14.5' + version = 'v0.14.6' 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 1732e774..9d7f4d39 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -168,7 +168,7 @@ engines: id: "docker" image: "rocker/r2u:24.04" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -225,11 +225,11 @@ build_info: output: "target/nextflow/report/create_report" executable: "target/nextflow/report/create_report/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -261,7 +261,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/report/create_report/_viash.yaml b/target/nextflow/report/create_report/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/report/create_report/_viash.yaml +++ b/target/nextflow/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 d2e2535e..ecba491a 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -1,4 +1,4 @@ -// create_report v0.14.5 +// create_report v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3261,7 +3261,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3334,12 +3334,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3357,7 +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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3849,7 +3849,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/report/create_report", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/create_report/nextflow.config b/target/nextflow/report/create_report/nextflow.config index 318831fd..4b9fd2b9 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 = 'v0.14.5' + version = 'v0.14.6' 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 4d5fe660..1e0da0c1 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -204,11 +204,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -240,7 +240,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/combine_star_logs/_viash.yaml b/target/nextflow/stats/combine_star_logs/_viash.yaml index ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 d421bb28..99bef693 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 v0.14.5 +// combine_star_logs v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3254,7 +3254,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3295,12 +3295,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/combine_star_logs", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3318,7 +3318,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3977,7 +3977,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/combine_star_logs", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/combine_star_logs/nextflow.config b/target/nextflow/stats/combine_star_logs/nextflow.config index 7fd8733c..76b269c6 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 = 'v0.14.5' + version = 'v0.14.6' 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 a30e6b0f..2f10e487 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: "v0.14.5" +version: "v0.14.6" 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: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -188,11 +188,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -224,7 +224,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_pool_statistics/_viash.yaml b/target/nextflow/stats/generate_pool_statistics/_viash.yaml index ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 f16a0b9d..7f48e20f 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 v0.14.5 +// generate_pool_statistics v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3279,12 +3279,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_pool_statistics", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3302,7 +3302,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3832,7 +3832,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_pool_statistics", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_pool_statistics/nextflow.config b/target/nextflow/stats/generate_pool_statistics/nextflow.config index ebbc3bb3..66c148b9 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 = 'v0.14.5' + version = 'v0.14.6' 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 b42ad131..aa3169fe 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -230,7 +230,7 @@ engines: id: "docker" image: "python:3.13-trixie" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -260,11 +260,11 @@ 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: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -296,7 +296,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_well_statistics/_viash.yaml b/target/nextflow/stats/generate_well_statistics/_viash.yaml index ba1471d3..7758cabb 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: v0.14.5 +version: v0.14.6 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 c893964f..e0ea51bd 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 v0.14.5 +// generate_well_statistics v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3319,7 +3319,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-trixie", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3361,12 +3361,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/stats/generate_well_statistics", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3384,7 +3384,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3905,7 +3905,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_well_statistics", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_well_statistics/nextflow.config b/target/nextflow/stats/generate_well_statistics/nextflow.config index 683bd34c..c937beb5 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 = 'v0.14.5' + version = 'v0.14.6' 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 f42eb43d..dcee1e58 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: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Arguments" arguments: @@ -160,13 +160,13 @@ build_info: output: "target/nextflow/utils/concatRuns" executable: "target/nextflow/utils/concatRuns/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/craftbox/v0.3.1/nextflow/concat_text" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -198,7 +198,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/concatRuns/_viash.yaml b/target/nextflow/utils/concatRuns/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/utils/concatRuns/_viash.yaml +++ b/target/nextflow/utils/concatRuns/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 f3dfb3c9..c756afc1 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -1,4 +1,4 @@ -// concatRuns v0.14.5 +// concatRuns v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "argument_groups" : [ { "name" : "Arguments", @@ -3229,12 +3229,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3252,7 +3252,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/utils/concatRuns/nextflow.config b/target/nextflow/utils/concatRuns/nextflow.config index 384e6756..29a7cdeb 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 = 'v0.14.5' + version = 'v0.14.6' description = 'Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n' } diff --git a/target/nextflow/utils/save_params/.config.vsh.yaml b/target/nextflow/utils/save_params/.config.vsh.yaml index 41a117ea..e22d535d 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: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Inputs" arguments: @@ -20,14 +20,23 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "string" + name: "--workflow_analysis" + description: "Base64 encoded YAML containing workflow analysis information (name\ + \ and version for all workflows)\n" + info: null + required: false + direction: "input" + multiple: false + multiple_sep: ";" - name: "Outputs" arguments: - type: "file" name: "--output" description: "The output YAML file\n" info: null - example: - - "output.yaml" + default: + - "params.yaml" must_exist: true create_parent: true required: true @@ -128,7 +137,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.5" + target_tag: "v0.14.6" namespace_separator: "/" setup: - type: "apt" @@ -151,11 +160,11 @@ build_info: output: "target/nextflow/utils/save_params" executable: "target/nextflow/utils/save_params/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -187,7 +196,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/save_params/_viash.yaml b/target/nextflow/utils/save_params/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/utils/save_params/_viash.yaml +++ b/target/nextflow/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 7ad41d41..ce392cb4 100644 --- a/target/nextflow/utils/save_params/main.nf +++ b/target/nextflow/utils/save_params/main.nf @@ -1,4 +1,4 @@ -// save_params v0.14.5 +// save_params v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "argument_groups" : [ { "name" : "Inputs", @@ -3054,6 +3054,15 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "string", + "name" : "--workflow_analysis", + "description" : "Base64 encoded YAML containing workflow analysis information (name and version for all workflows)\n", + "required" : false, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3064,8 +3073,8 @@ meta = [ "type" : "file", "name" : "--output", "description" : "The output YAML file\n", - "example" : [ - "output.yaml" + "default" : [ + "params.yaml" ], "must_exist" : true, "create_parent" : true, @@ -3192,7 +3201,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.5", + "target_tag" : "v0.14.6", "namespace_separator" : "/", "setup" : [ { @@ -3223,12 +3232,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/utils/save_params", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3246,7 +3255,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3286,6 +3295,7 @@ import base64 par = { 'id': $( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "r'${VIASH_PAR_ID//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), 'params_yaml': $( if [ ! -z ${VIASH_PAR_PARAMS_YAML+x} ]; then echo "r'${VIASH_PAR_PARAMS_YAML//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), + 'workflow_analysis': $( if [ ! -z ${VIASH_PAR_WORKFLOW_ANALYSIS+x} ]; then echo "r'${VIASH_PAR_WORKFLOW_ANALYSIS//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ), 'output': $( if [ ! -z ${VIASH_PAR_OUTPUT+x} ]; then echo "r'${VIASH_PAR_OUTPUT//\\'/\\'\\"\\'\\"r\\'}'"; else echo None; fi ) } meta = { @@ -3314,10 +3324,18 @@ dep = { ## VIASH END +# Custom representer to preserve dict order in YAML output +# Note: Python 3.7+ dicts maintain insertion order by default +def represent_dict(dumper, data): + return dumper.represent_dict(data.items()) + class Dumper(yaml.Dumper): def increase_indent(self, flow=False, indentless=False): return super(Dumper, self).increase_indent(flow, False) +# Register the representer for dicts to preserve order +Dumper.add_representer(dict, represent_dict) + def decode_params_yaml(encoded_yaml): yaml_bytes = base64.b64decode(encoded_yaml) yaml_string = yaml_bytes.decode('utf-8') @@ -3327,8 +3345,26 @@ def decode_params_yaml(encoded_yaml): params = decode_params_yaml(par['params_yaml']) +# Build the output structure +output_data = params # params is a list of states + +# Add workflow analysis information if provided +if par.get('workflow_analysis'): + try: + analysis_bytes = base64.b64decode(par['workflow_analysis']) + analysis_string = analysis_bytes.decode('utf-8') + analysis = yaml.safe_load(analysis_string) + # Since params is a list, create a dict wrapper + output_data = { + 'params': params, + 'analysis': analysis + } + except (TypeError, ValueError) as e: + e.add_note("Could not parse workflow_analysis YAML.") + raise + with open(par["output"], 'w') as f: - yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) + yaml.dump(output_data, f, default_flow_style=False, Dumper=Dumper) VIASHMAIN python -B "$tempscript" ''' @@ -3711,7 +3747,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/utils/save_params", - "tag" : "v0.14.5" + "tag" : "v0.14.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/utils/save_params/nextflow.config b/target/nextflow/utils/save_params/nextflow.config index 3e8e7c8f..83423f42 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 = 'v0.14.5' + version = 'v0.14.6' description = 'Save parameters to a YAML file\n' } diff --git a/target/nextflow/utils/save_params/nextflow_schema.json b/target/nextflow/utils/save_params/nextflow_schema.json index d6f579fc..6aa7a23b 100644 --- a/target/nextflow/utils/save_params/nextflow_schema.json +++ b/target/nextflow/utils/save_params/nextflow_schema.json @@ -18,6 +18,11 @@ "type": "string", "description": "base64 encoded yaml containing the state\n", "help_text": "Type: `string`, multiple: `False`, required. " + }, + "workflow_analysis": { + "type": "string", + "description": "Base64 encoded YAML containing workflow analysis information (name and version for all workflows)\n", + "help_text": "Type: `string`, multiple: `False`. " } } }, @@ -30,8 +35,8 @@ "type": "string", "format": "path", "description": "The output YAML file\n", - "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.yaml\"`, direction: `output`, example: `\"output.yaml\"`. ", - "default": "$id.$key.output.yaml" + "help_text": "Type: `file`, multiple: `False`, required, default: `\"params.yaml\"`, direction: `output`. ", + "default": "params.yaml" } } }, diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index 66dc0ede..8a679d32 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -326,7 +326,7 @@ build_info: output: "target/nextflow/workflows/htrnaseq" executable: "target/nextflow/workflows/htrnaseq/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/nextflow/workflows/well_demultiplex" @@ -334,7 +334,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -366,7 +366,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/htrnaseq/_viash.yaml b/target/nextflow/workflows/htrnaseq/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/workflows/htrnaseq/_viash.yaml +++ b/target/nextflow/workflows/htrnaseq/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 9c162a88..5d469ecd 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -1,4 +1,4 @@ -// htrnaseq v0.14.5 +// htrnaseq v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3442,12 +3442,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3465,7 +3465,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/htrnaseq/nextflow.config b/target/nextflow/workflows/htrnaseq/nextflow.config index 2c3b0f48..ff3194a5 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 = 'v0.14.5' + version = 'v0.14.6' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index bf7db204..41a35064 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: "v0.14.5" +version: "v0.14.6" argument_groups: - name: "Input arguments" arguments: @@ -337,7 +337,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/_private/nextflow/utils/listInputDir" @@ -348,7 +348,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -380,7 +380,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/runner/_viash.yaml b/target/nextflow/workflows/runner/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/workflows/runner/_viash.yaml +++ b/target/nextflow/workflows/runner/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 d1e9fdd9..cf40dc01 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.14.5 +// runner v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3452,12 +3452,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3475,7 +3475,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", @@ -3516,8 +3516,6 @@ def date = new Date().format('yyyyMMdd_hhmmss') session = nextflow.Nextflow.getSession() final service = session.publishDirExecutorService() - - def viash_config = java.nio.file.Paths.get("${moduleDir}/_viash.yaml") def version = get_version(viash_config) @@ -3531,6 +3529,33 @@ def regex_trailing_slashes = ~/\/+$/ def results_publish_dir = params.results_publish_dir - regex_trailing_slashes def fastq_publish_dir = params.fastq_publish_dir - regex_trailing_slashes +def get_workflow_analysis() { + def dependencies = [] + + if (meta.config.dependencies) { + meta.config.dependencies.each { dep_spec -> + def dependency_name = dep_spec.alias ? dep_spec.alias : dep_spec.name + def dependency_var = file(dependency_name).name + def dependency = binding.getVariable(dependency_var) + + def dep_entry = new LinkedHashMap() + dep_entry.name = dependency.config.name ?: "unknown_name" + dep_entry.version = dependency.config.version ?: "unknown_version" + dependencies << dep_entry + } + } + + // Build main analysis entry with dependencies using LinkedHashMap for order + def main_entry = new LinkedHashMap() + main_entry.name = meta.config.name ?: "unknown_name" + main_entry.version = meta.config.version ?: "unknown_version" + main_entry.dependencies = dependencies + + def analysis = [main_entry] + + println("Analysis workflows: ${analysis}") + return analysis +} /* This is a utility workflow that gathers the input events and saves their state to a YAML file. @@ -3554,7 +3579,6 @@ workflow save_params_wf { | save_params.run( key: "save_params_runner", fromState: {id, state -> - def convertPaths convertPaths = { value -> if (value instanceof java.nio.file.Path) @@ -3574,13 +3598,19 @@ workflow save_params_wf { def yamlString = yaml.dump(convertedState) def encodedYaml = yamlString.bytes.encodeBase64().toString() + def yaml_builder = new org.yaml.snakeyaml.Yaml() + def analysis_yaml = yaml_builder.dump(get_workflow_analysis()) + def encoded_analysis = analysis_yaml.bytes.encodeBase64().toString() + return [ "id": id, "params_yaml": encodedYaml, - "output": state.run_params + "workflow_analysis": encoded_analysis ] }, - toState: ["run_params": "output"] + toState: { id, output, state -> + state + [ run_params: output.output ] + } ) emit: diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config index ae68c5b3..9435a59a 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 = 'v0.14.5' + version = 'v0.14.6' 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 9235c818..09259948 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -222,7 +222,7 @@ build_info: output: "target/nextflow/workflows/well_demultiplex" executable: "target/nextflow/workflows/well_demultiplex/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.4.2/nextflow/cutadapt" @@ -230,7 +230,7 @@ build_info: - "target/dependencies/vsh/vsh/craftbox/v0.3.1/nextflow/move_files_to_directory" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -262,7 +262,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_demultiplex/_viash.yaml b/target/nextflow/workflows/well_demultiplex/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/workflows/well_demultiplex/_viash.yaml +++ b/target/nextflow/workflows/well_demultiplex/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 da313016..e3c579ef 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -1,4 +1,4 @@ -// well_demultiplex v0.14.5 +// well_demultiplex v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3327,12 +3327,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_demultiplex", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3350,7 +3350,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_demultiplex/nextflow.config b/target/nextflow/workflows/well_demultiplex/nextflow.config index 0f8931de..a1ce9d40 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 = 'v0.14.5' + version = 'v0.14.6' 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 59cf2907..eb9194f2 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: "v0.14.5" +version: "v0.14.6" authors: - name: "Dries Schaumont" roles: @@ -215,11 +215,11 @@ build_info: output: "target/nextflow/workflows/well_metadata" executable: "target/nextflow/workflows/well_metadata/main.nf" viash_version: "0.9.4" - git_commit: "9d5018b257513e527f13faf524f1e9e6df01c465" + git_commit: "9346c55e3f894994935b0928759dca9e56866d37" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.5" + version: "v0.14.6" 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\ @@ -251,7 +251,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_metadata/_viash.yaml b/target/nextflow/workflows/well_metadata/_viash.yaml index ba1471d3..7758cabb 100644 --- a/target/nextflow/workflows/well_metadata/_viash.yaml +++ b/target/nextflow/workflows/well_metadata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.5 +version: v0.14.6 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 a7e24b58..f4cc4ee4 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -1,4 +1,4 @@ -// well_metadata v0.14.5 +// well_metadata v0.14.6 // // 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" : "v0.14.5", + "version" : "v0.14.6", "authors" : [ { "name" : "Dries Schaumont", @@ -3299,12 +3299,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/well_metadata", "viash_version" : "0.9.4", - "git_commit" : "9d5018b257513e527f13faf524f1e9e6df01c465", + "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.5", + "version" : "v0.14.6", "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" : { @@ -3322,7 +3322,7 @@ 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 := 'v0.14.5'" + ".engines[.type == 'docker'].target_tag := 'v0.14.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_metadata/nextflow.config b/target/nextflow/workflows/well_metadata/nextflow.config index 04f895f3..ea192e93 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 = 'v0.14.5' + version = 'v0.14.6' author = 'Dries Schaumont' }