From 8bc82c81e336f7b01ee3a0c406ea61d87e222a8b Mon Sep 17 00:00:00 2001 From: CI Date: Thu, 2 Apr 2026 14:08:44 +0000 Subject: [PATCH] Build branch htrnaseq/v0.14 with version v0.14.7 to htrnaseq on branch v0.14 (07ba686) Build pipeline: viash-hub.htrnaseq.v0.14.7-lr47z Source commit: https://github.com/viash-hub/htrnaseq/commit/07ba686a4603dac053f3e9f9990081cdb506169e Source message: Bump version to v0.14.7 --- CHANGELOG.md | 6 ++ _viash.yaml | 2 +- src/io/publish_results/code.sh | 1 + src/io/publish_results/config.vsh.yaml | 6 ++ src/utils/save_params/config.vsh.yaml | 7 +- src/utils/save_params/script.py | 29 +----- src/workflows/runner/config.vsh.yaml | 6 ++ src/workflows/runner/main.nf | 66 ++++++++++---- .../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 | 28 ++++-- .../executable/io/publish_results/_viash.yaml | 2 +- .../io/publish_results/publish_results | 75 ++++++++++++++-- .../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 | 28 ++++-- .../nextflow/io/publish_results/_viash.yaml | 2 +- target/nextflow/io/publish_results/main.nf | 37 ++++++-- .../io/publish_results/nextflow.config | 2 +- .../io/publish_results/nextflow_schema.json | 14 +++ 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 | 21 ++++- target/nextflow/workflows/runner/_viash.yaml | 2 +- target/nextflow/workflows/runner/main.nf | 90 ++++++++++++++----- .../nextflow/workflows/runner/nextflow.config | 2 +- .../workflows/runner/nextflow_schema.json | 7 ++ .../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 +- 130 files changed, 729 insertions(+), 608 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f9c1b693..38202ecd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# htrnaseq v0.14.7 + +## Bug fixes + +* Revert breaking changes from PR #95 and re-implement writing (sub-)workflow version to a separate file (PR #103). + # htrnaseq v0.14.6 ## Minor changes diff --git a/_viash.yaml b/_viash.yaml index 7758cabb..e4186d40 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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/io/publish_results/code.sh b/src/io/publish_results/code.sh index e3a4242e..d6dfffeb 100755 --- a/src/io/publish_results/code.sh +++ b/src/io/publish_results/code.sh @@ -19,6 +19,7 @@ declare -A path_pars_dirs=( declare -A path_pars_files=( ["par_html_report_output"]="par_html_report" ["par_run_params_output"]="par_run_params" + ["par_run_metadata_output"]="par_run_metadata" ) echo "Canonicalizing output paths." diff --git a/src/io/publish_results/config.vsh.yaml b/src/io/publish_results/config.vsh.yaml index 6da4c312..db178391 100644 --- a/src/io/publish_results/config.vsh.yaml +++ b/src/io/publish_results/config.vsh.yaml @@ -35,6 +35,9 @@ argument_groups: - name: "--run_params" type: file required: true + - name: "--run_metadata" + type: file + required: true - name: Output directory description: | Determines the name of output directories @@ -69,6 +72,9 @@ argument_groups: - name: "--run_params_output" type: file direction: output + - name: "--run_metadata_output" + type: file + direction: output - name: "--html_report_output" type: file direction: output diff --git a/src/utils/save_params/config.vsh.yaml b/src/utils/save_params/config.vsh.yaml index 0739ce75..d21924da 100644 --- a/src/utils/save_params/config.vsh.yaml +++ b/src/utils/save_params/config.vsh.yaml @@ -16,11 +16,6 @@ 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: @@ -28,9 +23,9 @@ 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 2eeec623..0eed41d9 100644 --- a/src/utils/save_params/script.py +++ b/src/utils/save_params/script.py @@ -6,23 +6,14 @@ 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') @@ -32,24 +23,6 @@ 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(output_data, f, default_flow_style=False, Dumper=Dumper) + yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) diff --git a/src/workflows/runner/config.vsh.yaml b/src/workflows/runner/config.vsh.yaml index e63e144b..044730be 100644 --- a/src/workflows/runner/config.vsh.yaml +++ b/src/workflows/runner/config.vsh.yaml @@ -73,6 +73,12 @@ argument_groups: type: file direction: output default: params.yaml + - name: "--run_metadata" + type: file + description: | + YAML file containing meta information about the file — .e.g. versions of (sub)-workflows. + direction: output + default: metadata.yaml - name: "--star_output_dir" type: file direction: output diff --git a/src/workflows/runner/main.nf b/src/workflows/runner/main.nf index 7796c2c5..54ce712f 100644 --- a/src/workflows/runner/main.nf +++ b/src/workflows/runner/main.nf @@ -36,17 +36,20 @@ def get_workflow_analysis() { } // 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 main_entry = [ + "name": meta.config.name ?: "unknown_name", + "version": meta.config.version ?: "unknown_version", + "dependencies": dependencies + ] - def analysis = [main_entry] + def analysis = ["versions": [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. */ @@ -63,12 +66,21 @@ workflow save_params_wf { def all_states = states.collect{it[1]} def run_params_output_templates = all_states.collect{it.run_params} assert run_params_output_templates.unique().size() == 1: "The value for the 'run_params' parameter is not the same across runs." - def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states] + + def run_metadata_output_templates = all_states.collect{it.run_metadata} + assert run_metadata_output_templates.unique().size() == 1: "The value for the 'run_metadata' parameter is not the same across runs." + + def new_state = [ + "run_params": run_params_output_templates[0], + "run_metadata": run_metadata_output_templates[0], + "all_states": all_states + ] return [new_id, new_state] } | save_params.run( key: "save_params_runner", fromState: {id, state -> + def convertPaths convertPaths = { value -> if (value instanceof java.nio.file.Path) @@ -88,21 +100,32 @@ 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, - "workflow_analysis": encoded_analysis + "output": state.run_params + ] + }, + toState: ["run_params": "output"] + ) + | save_params.run( + key: "save_meta_runner", + fromState: {id, state -> + 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": encoded_analysis, + "output": state.run_metadata, ] }, toState: { id, output, state -> - state + [ run_params: output.output ] + state + [ run_metadata: output.output ] } ) + emit: output_ch } @@ -301,7 +324,8 @@ workflow run_wf { "eset_dir", "f_data_dir", "p_data_dir", - "run_params" + "run_params", + "run_metadata" ] def new_state = demux_state + input_state.subMap(keys_to_transfer) @@ -312,7 +336,8 @@ workflow run_wf { "eset_dir", "f_data_dir", "p_data_dir", - "run_params" + "run_params", + "run_metadata" ] new_state = new_state.collectEntries{k, v -> def newKey = keys_to_rename.contains(k) ? "${k}_workflow" : k @@ -398,7 +423,10 @@ workflow run_wf { // Add the run parameter YAML to the output | map {id, grouped_ch_state, _, save_params_state -> assert save_params_state.run_params.isFile() - def new_state = grouped_ch_state + ["run_params": save_params_state.run_params] + def new_state = grouped_ch_state + [ + "run_params": save_params_state.run_params, + "run_metadata": save_params_state.run_metadata + ] return [id, new_state] } // Group the events in order to publish the results per experiment @@ -436,8 +464,10 @@ workflow run_wf { "f_data_dir_workflow", "p_data_dir_workflow", "run_params_workflow", + "run_metadata_workflow", "f_data", - "run_params" + "run_params", + "run_metadata" ] def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name -> argument_values = states.collect{it.get(argument_name)}.unique() @@ -480,9 +510,11 @@ workflow run_wf { p_data: state.p_data, html_report: state.html_report, run_params: state.run_params, + run_metadata: state.run_metadata, // Output locations html_report_output: "${state.results_prefix}/${state.html_report.name}", run_params_output: "${state.results_prefix}/${state.run_params_workflow}", + run_metadata_output: "${state.results_prefix}/${state.run_metadata_workflow}", star_output_dir: "${state.results_prefix}/${state.star_output_dir_workflow}", nrReadsNrGenesPerChrom_dir: "${state.results_prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}", star_qc_metrics_dir: "${state.results_prefix}/${state.star_qc_metrics_dir_workflow}", @@ -494,6 +526,7 @@ workflow run_wf { toState: { id, result, state -> result + [ "run_params": state.run_params, + "run_metadata": state.run_metadata, "_meta": ["join_id": state.event_id[0]], "results_prefix": state.results_prefix ] @@ -598,6 +631,7 @@ workflow run_wf { "f_data_dir", "p_data_dir", "run_params", + "run_metadata", "_meta" ] ) diff --git a/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml b/target/_private/nextflow/utils/listInputDir/.config.vsh.yaml index d7a2c4c2..f70f4274 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: "v0.14.6" +version: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/_private/nextflow/utils/listInputDir/_viash.yaml b/target/_private/nextflow/utils/listInputDir/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/_private/nextflow/utils/listInputDir/_viash.yaml +++ b/target/_private/nextflow/utils/listInputDir/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 0f65798f..f86ae3fc 100644 --- a/target/_private/nextflow/utils/listInputDir/main.nf +++ b/target/_private/nextflow/utils/listInputDir/main.nf @@ -1,4 +1,4 @@ -// listInputDir v0.14.6 +// listInputDir v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", diff --git a/target/_private/nextflow/utils/listInputDir/nextflow.config b/target/_private/nextflow/utils/listInputDir/nextflow.config index 83b27cf1..62ff4d29 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 = 'v0.14.6' + version = 'v0.14.7' 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 d67c3b92..acc6673a 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: "v0.14.6" +version: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" 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: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" 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 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 300af4e6..c8d7df5b 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 v0.14.6 +// well_fastqs_to_esets v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "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 0c3e216e..4075d0ca 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 = 'v0.14.6' + version = 'v0.14.7' 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 e5d55a94..1ca5a562 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_eset/_viash.yaml b/target/executable/eset/create_eset/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/eset/create_eset/_viash.yaml +++ b/target/executable/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 3b02753f..61111f45 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 v0.14.6 +# create_eset v0.14.7 # # 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="2026-02-23T13:37:11Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_eset v0.14.6" + echo "create_eset v0.14.7" echo "" echo "Arguments:" echo " --pDataFile" @@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_eset v0.14.6" + echo "create_eset v0.14.7" exit ;; --pDataFile) @@ -794,7 +794,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.14.7' fi # print dockerfile diff --git a/target/executable/eset/create_fdata/.config.vsh.yaml b/target/executable/eset/create_fdata/.config.vsh.yaml index b8a0597f..5b197a39 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_fdata/_viash.yaml b/target/executable/eset/create_fdata/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/eset/create_fdata/_viash.yaml +++ b/target/executable/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 fd1f88f3..12cf88e7 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 v0.14.6 +# create_fdata v0.14.7 # # 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="2026-02-23T13:37:11Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_fdata v0.14.6" + echo "create_fdata v0.14.7" echo "" echo "Create a fdata file" echo "" @@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_fdata v0.14.6" + echo "create_fdata v0.14.7" exit ;; --gtf) @@ -756,7 +756,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.14.7' fi # print dockerfile diff --git a/target/executable/eset/create_pdata/.config.vsh.yaml b/target/executable/eset/create_pdata/.config.vsh.yaml index a3538e27..5485f80f 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/eset/create_pdata/_viash.yaml b/target/executable/eset/create_pdata/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/eset/create_pdata/_viash.yaml +++ b/target/executable/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 8b53cfa0..1e967588 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 v0.14.6 +# create_pdata v0.14.7 # # 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="2026-02-23T13:37:11Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_pdata v0.14.6" + echo "create_pdata v0.14.7" echo "" echo "Create a pdata file by combining the mapping statistics" echo "" @@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_pdata v0.14.6" + echo "create_pdata v0.14.7" exit ;; --star_stats_file) @@ -777,7 +777,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.14.7' 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 d4773c19..35480abe 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" 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 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 80b84b1e..2d1dd998 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 v0.14.6 +# check_eset v0.14.7 # # 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="2026-02-23T13:37:11Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "check_eset v0.14.6" + echo "check_eset v0.14.7" echo "" echo "This component test the ExpressionSet object as output by the main pipeline." echo "" @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_eset v0.14.6" + echo "check_eset v0.14.7" exit ;; --eset) @@ -754,7 +754,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.14.7' 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 20dc61d5..59c61522 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" 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 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 ceed99f0..b18f86c8 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 v0.14.6 +# check_cutadapt_output v0.14.7 # # 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="2026-02-23T13:37:11Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" 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 v0.14.6" + echo "check_cutadapt_output v0.14.7" echo "" echo "This component test the cutadapt output from the well_demultiplex subworkflow." echo "" @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "check_cutadapt_output v0.14.6" + echo "check_cutadapt_output v0.14.7" exit ;; --fastq_r1) @@ -783,7 +783,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.14.7' fi # print dockerfile diff --git a/target/executable/io/publish_fastqs/.config.vsh.yaml b/target/executable/io/publish_fastqs/.config.vsh.yaml index 2891b7e7..70a34497 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_fastqs/_viash.yaml b/target/executable/io/publish_fastqs/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/io/publish_fastqs/_viash.yaml +++ b/target/executable/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 3a429dc2..0c6343c2 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 v0.14.6 +# publish_fastqs v0.14.7 # # 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="2026-02-23T13:37:12Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_fastqs v0.14.6" + echo "publish_fastqs v0.14.7" echo "" echo "Publish the fastq files per well" echo "" @@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_fastqs v0.14.6" + echo "publish_fastqs v0.14.7" exit ;; --input) @@ -750,7 +750,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.14.7' fi # print dockerfile diff --git a/target/executable/io/publish_results/.config.vsh.yaml b/target/executable/io/publish_results/.config.vsh.yaml index ca918ed1..7e92dfd2 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: "v0.14.6" +version: "v0.14.7" argument_groups: - name: "Input arguments" arguments: @@ -77,6 +77,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--run_metadata" + info: null + must_exist: true + create_parent: true + required: true + direction: "input" + multiple: false + multiple_sep: ";" - name: "Output directory" description: "Determines the name of output directories\n" arguments: @@ -158,6 +167,15 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--run_metadata_output" + info: null + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--html_report_output" info: null @@ -261,7 +279,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.6" + target_tag: "v0.14.7" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +297,11 @@ build_info: output: "target/executable/io/publish_results" executable: "target/executable/io/publish_results/publish_results" viash_version: "0.9.4" - git_commit: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 +333,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/io/publish_results/_viash.yaml b/target/executable/io/publish_results/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/io/publish_results/_viash.yaml +++ b/target/executable/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 9bf6d780..71d6e2c6 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 v0.14.6 +# publish_results v0.14.7 # # 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="2026-02-23T13:37:12Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish_results v0.14.6" + echo "publish_results v0.14.7" echo "" echo "Publish the results" echo "" @@ -600,6 +600,9 @@ function ViashHelp { echo " --run_params" echo " type: file, required parameter, file must exist" echo "" + echo " --run_metadata" + echo " type: file, required parameter, file must exist" + echo "" echo "Output directory:" echo " Determines the name of output directories" echo "" @@ -633,6 +636,9 @@ function ViashHelp { echo " --run_params_output" echo " type: file, output, file must exist" echo "" + echo " --run_metadata_output" + echo " type: file, output, file must exist" + echo "" echo " --html_report_output" echo " type: file, output, file must exist" echo "" @@ -683,7 +689,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish_results v0.14.6" + echo "publish_results v0.14.7" exit ;; --star_output) @@ -810,6 +816,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_RUN_PARAMS=$(ViashRemoveFlags "$1") shift 1 ;; + --run_metadata) + [ -n "$VIASH_PAR_RUN_METADATA" ] && ViashError Bad arguments for option \'--run_metadata\': \'$VIASH_PAR_RUN_METADATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RUN_METADATA="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_metadata. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --run_metadata=*) + [ -n "$VIASH_PAR_RUN_METADATA" ] && ViashError Bad arguments for option \'--run_metadata=*\': \'$VIASH_PAR_RUN_METADATA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RUN_METADATA=$(ViashRemoveFlags "$1") + shift 1 + ;; --star_output_dir) [ -n "$VIASH_PAR_STAR_OUTPUT_DIR" ] && ViashError Bad arguments for option \'--star_output_dir\': \'$VIASH_PAR_STAR_OUTPUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_STAR_OUTPUT_DIR="$2" @@ -887,6 +904,17 @@ while [[ $# -gt 0 ]]; do VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashRemoveFlags "$1") shift 1 ;; + --run_metadata_output) + [ -n "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && ViashError Bad arguments for option \'--run_metadata_output\': \'$VIASH_PAR_RUN_METADATA_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RUN_METADATA_OUTPUT="$2" + [ $# -lt 2 ] && ViashError Not enough arguments passed to --run_metadata_output. Use "--help" to get more information on the parameters. && exit 1 + shift 2 + ;; + --run_metadata_output=*) + [ -n "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && ViashError Bad arguments for option \'--run_metadata_output=*\': \'$VIASH_PAR_RUN_METADATA_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 + VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashRemoveFlags "$1") + shift 1 + ;; --html_report_output) [ -n "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && ViashError Bad arguments for option \'--html_report_output\': \'$VIASH_PAR_HTML_REPORT_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1 VIASH_PAR_HTML_REPORT_OUTPUT="$2" @@ -986,7 +1014,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.14.7' fi # print dockerfile @@ -1102,6 +1130,10 @@ if [ -z ${VIASH_PAR_RUN_PARAMS+x} ]; then ViashError '--run_params' is a required argument. Use "--help" to get more information on the parameters. exit 1 fi +if [ -z ${VIASH_PAR_RUN_METADATA+x} ]; then + ViashError '--run_metadata' is a required argument. Use "--help" to get more information on the parameters. + exit 1 +fi if [ -z ${VIASH_META_NAME+x} ]; then ViashError 'name' is a required argument. Use "--help" to get more information on the parameters. exit 1 @@ -1228,6 +1260,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS" ]; then ViashError "Input file '$VIASH_PAR_RUN_PARAMS' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_RUN_METADATA" ] && [ ! -e "$VIASH_PAR_RUN_METADATA" ]; then + ViashError "Input file '$VIASH_PAR_RUN_METADATA' does not exist." + exit 1 +fi # check whether parameters values are of the right type if [[ -n "$VIASH_META_CPUS" ]]; then @@ -1325,6 +1361,9 @@ fi if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")" ]; then mkdir -p "$(dirname "$VIASH_PAR_RUN_PARAMS_OUTPUT")" fi +if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_RUN_METADATA_OUTPUT")" ]; then + mkdir -p "$(dirname "$VIASH_PAR_RUN_METADATA_OUTPUT")" +fi if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")" ]; then mkdir -p "$(dirname "$VIASH_PAR_HTML_REPORT_OUTPUT")" fi @@ -1415,6 +1454,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_PARAMS")" ) VIASH_PAR_RUN_PARAMS=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS") fi +if [ ! -z "$VIASH_PAR_RUN_METADATA" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_METADATA")" ) + VIASH_PAR_RUN_METADATA=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_METADATA") +fi if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_STAR_OUTPUT_DIR")" ) VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerAutodetectMount "$VIASH_PAR_STAR_OUTPUT_DIR") @@ -1450,6 +1493,11 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_PARAMS_OUTPUT") VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_PARAMS_OUTPUT" ) fi +if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then + VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RUN_METADATA_OUTPUT")" ) + VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_RUN_METADATA_OUTPUT") + VIASH_CHOWN_VARS+=( "$VIASH_PAR_RUN_METADATA_OUTPUT" ) +fi if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_HTML_REPORT_OUTPUT")" ) VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_HTML_REPORT_OUTPUT") @@ -1532,6 +1580,7 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#' $( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi ) $( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi ) $( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; fi ) +$( if [ ! -z ${VIASH_PAR_RUN_METADATA+x} ]; then echo "${VIASH_PAR_RUN_METADATA}" | sed "s#'#'\"'\"'#g;s#.*#par_run_metadata='&'#" ; else echo "# par_run_metadata="; fi ) $( if [ ! -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi ) $( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi ) $( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi ) @@ -1539,6 +1588,7 @@ $( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed $( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi ) $( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\"'\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi ) $( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi ) +$( if [ ! -z ${VIASH_PAR_RUN_METADATA_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_METADATA_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_run_metadata_output='&'#" ; else echo "# par_run_metadata_output="; fi ) $( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) @@ -1581,6 +1631,7 @@ declare -A path_pars_dirs=( declare -A path_pars_files=( ["par_html_report_output"]="par_html_report" ["par_run_params_output"]="par_run_params" + ["par_run_metadata_output"]="par_run_metadata" ) echo "Canonicalizing output paths." @@ -1720,6 +1771,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_RUN_PARAMS" ]; then VIASH_PAR_RUN_PARAMS=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS") fi + if [ ! -z "$VIASH_PAR_RUN_METADATA" ]; then + VIASH_PAR_RUN_METADATA=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_METADATA") + fi if [ ! -z "$VIASH_PAR_STAR_OUTPUT_DIR" ]; then VIASH_PAR_STAR_OUTPUT_DIR=$(ViashDockerStripAutomount "$VIASH_PAR_STAR_OUTPUT_DIR") fi @@ -1741,6 +1795,9 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ]; then VIASH_PAR_RUN_PARAMS_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_PARAMS_OUTPUT") fi + if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then + VIASH_PAR_RUN_METADATA_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_RUN_METADATA_OUTPUT") + fi if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then VIASH_PAR_HTML_REPORT_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_HTML_REPORT_OUTPUT") fi @@ -1788,6 +1845,10 @@ if [ ! -z "$VIASH_PAR_RUN_PARAMS_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_PARAMS_OUTP ViashError "Output file '$VIASH_PAR_RUN_PARAMS_OUTPUT' does not exist." exit 1 fi +if [ ! -z "$VIASH_PAR_RUN_METADATA_OUTPUT" ] && [ ! -e "$VIASH_PAR_RUN_METADATA_OUTPUT" ]; then + ViashError "Output file '$VIASH_PAR_RUN_METADATA_OUTPUT' does not exist." + exit 1 +fi if [ ! -z "$VIASH_PAR_HTML_REPORT_OUTPUT" ] && [ ! -e "$VIASH_PAR_HTML_REPORT_OUTPUT" ]; then ViashError "Output file '$VIASH_PAR_HTML_REPORT_OUTPUT' does not exist." exit 1 diff --git a/target/executable/parallel_map/.config.vsh.yaml b/target/executable/parallel_map/.config.vsh.yaml index 227987ee..fddc7a37 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: "v0.14.6" +version: "v0.14.7" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/parallel_map/_viash.yaml b/target/executable/parallel_map/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/parallel_map/_viash.yaml +++ b/target/executable/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 6ad312cb..4051239d 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 v0.14.6 +# parallel_map v0.14.7 # # 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="2026-02-23T13:37:11Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:01Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "parallel_map v0.14.6" + echo "parallel_map v0.14.7" echo "" echo "Map wells in batch, using STAR" echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin" @@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "parallel_map v0.14.6" + echo "parallel_map v0.14.7" exit ;; --input_r1) @@ -907,7 +907,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.14.7' fi # print dockerfile diff --git a/target/executable/report/create_report/.config.vsh.yaml b/target/executable/report/create_report/.config.vsh.yaml index 467f06e1..87fd9b36 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/report/create_report/_viash.yaml b/target/executable/report/create_report/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/report/create_report/_viash.yaml +++ b/target/executable/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 d5e51654..ec67011f 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 v0.14.6 +# create_report v0.14.7 # # 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="2026-02-23T13:37:10Z" +LABEL org.opencontainers.image.created="2026-04-02T13:02:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "create_report v0.14.6" + echo "create_report v0.14.7" echo "" echo "Create a basic QC report in HTML format based on a number of esets." echo "" @@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "create_report v0.14.6" + echo "create_report v0.14.7" exit ;; --eset) @@ -777,7 +777,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.14.7' 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 ef460bed..33121178 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/combine_star_logs/_viash.yaml b/target/executable/stats/combine_star_logs/_viash.yaml index 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 92fa8372..2bf38ecd 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 v0.14.6 +# combine_star_logs v0.14.7 # # 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="2026-02-23T13:37:10Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" 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 v0.14.6" + echo "combine_star_logs v0.14.7" echo "" echo "Arguments:" echo " --barcodes" @@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "combine_star_logs v0.14.6" + echo "combine_star_logs v0.14.7" exit ;; --barcodes) @@ -825,7 +825,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.14.7' 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 fb393839..69e86068 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_pool_statistics/_viash.yaml b/target/executable/stats/generate_pool_statistics/_viash.yaml index 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 a810a034..6e84a81d 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 v0.14.6 +# generate_pool_statistics v0.14.7 # # 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="2026-02-23T13:37:10Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" 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 v0.14.6" + echo "generate_pool_statistics v0.14.7" echo "" echo "Arguments:" echo " --nrReadsNrGenesPerChrom" @@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_pool_statistics v0.14.6" + echo "generate_pool_statistics v0.14.7" exit ;; --nrReadsNrGenesPerChrom) @@ -767,7 +767,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.14.7' 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 d841de03..824c07e8 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/stats/generate_well_statistics/_viash.yaml b/target/executable/stats/generate_well_statistics/_viash.yaml index 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 348895fb..4ab1acc1 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 v0.14.6 +# generate_well_statistics v0.14.7 # # 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="2026-02-23T13:37:10Z" +LABEL org.opencontainers.image.created="2026-04-02T13:02:59Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" 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 v0.14.6" + echo "generate_well_statistics v0.14.7" echo "" echo "Generate summary statistics from BAM files generated by STAR solo." echo "" @@ -682,7 +682,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "generate_well_statistics v0.14.6" + echo "generate_well_statistics v0.14.7" exit ;; --input) @@ -861,7 +861,7 @@ if [[ "$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:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.14.7' fi # print dockerfile diff --git a/target/executable/utils/save_params/.config.vsh.yaml b/target/executable/utils/save_params/.config.vsh.yaml index eae8243c..cf354a6f 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: "v0.14.6" +version: "v0.14.7" argument_groups: - name: "Inputs" arguments: @@ -20,23 +20,14 @@ 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 - default: - - "params.yaml" + example: + - "output.yaml" must_exist: true create_parent: true required: true @@ -137,7 +128,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.6" + target_tag: "v0.14.7" namespace_separator: "/" setup: - type: "apt" @@ -160,11 +151,11 @@ build_info: output: "target/executable/utils/save_params" executable: "target/executable/utils/save_params/save_params" viash_version: "0.9.4" - git_commit: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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\ @@ -196,7 +187,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/executable/utils/save_params/_viash.yaml b/target/executable/utils/save_params/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/executable/utils/save_params/_viash.yaml +++ b/target/executable/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 704f05f5..36697e93 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 v0.14.6 +# save_params v0.14.7 # # 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="2026-02-23T13:37:10Z" +LABEL org.opencontainers.image.created="2026-04-02T13:03:00Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq" -LABEL org.opencontainers.image.revision="9346c55e3f894994935b0928759dca9e56866d37" -LABEL org.opencontainers.image.version="v0.14.6" +LABEL org.opencontainers.image.revision="07ba686a4603dac053f3e9f9990081cdb506169e" +LABEL org.opencontainers.image.version="v0.14.7" VIASHDOCKER fi @@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm) # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "save_params v0.14.6" + echo "save_params v0.14.7" echo "" echo "Save parameters to a YAML file" echo "" @@ -586,15 +586,10 @@ 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 " default: params.yaml" + echo " example: output.yaml" echo " The output YAML file" echo "" echo "Viash built in Computational Requirements:" @@ -644,7 +639,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "save_params v0.14.6" + echo "save_params v0.14.7" exit ;; --id) @@ -669,17 +664,6 @@ 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="$2" @@ -779,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.6' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.14.7' fi # print dockerfile @@ -1072,7 +1056,6 @@ 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 = { @@ -1101,18 +1084,10 @@ 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') @@ -1122,26 +1097,8 @@ 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(output_data, f, default_flow_style=False, Dumper=Dumper) + yaml.dump(params, 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 99521e46..4ee56fac 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_eset/_viash.yaml b/target/nextflow/eset/create_eset/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/eset/create_eset/_viash.yaml +++ b/target/nextflow/eset/create_eset/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 c143516c..67cd4dd0 100644 --- a/target/nextflow/eset/create_eset/main.nf +++ b/target/nextflow/eset/create_eset/main.nf @@ -1,4 +1,4 @@ -// create_eset v0.14.6 +// create_eset v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3271,7 +3271,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3309,12 +3309,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_eset", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -4217,7 +4217,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_eset", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_eset/nextflow.config b/target/nextflow/eset/create_eset/nextflow.config index 3c9fb93d..b1b6dd87 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 = 'v0.14.6' + version = 'v0.14.7' 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 25c9dac0..b092e932 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_fdata/_viash.yaml b/target/nextflow/eset/create_fdata/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/eset/create_fdata/_viash.yaml +++ b/target/nextflow/eset/create_fdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 9bbffc2c..ad6725c5 100644 --- a/target/nextflow/eset/create_fdata/main.nf +++ b/target/nextflow/eset/create_fdata/main.nf @@ -1,4 +1,4 @@ -// create_fdata v0.14.6 +// create_fdata v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3279,12 +3279,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_fdata", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3872,7 +3872,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_fdata", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_fdata/nextflow.config b/target/nextflow/eset/create_fdata/nextflow.config index 81620665..7d77d02f 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 = 'v0.14.6' + version = 'v0.14.7' 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 ac7b411a..18f07b90 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/eset/create_pdata/_viash.yaml b/target/nextflow/eset/create_pdata/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/eset/create_pdata/_viash.yaml +++ b/target/nextflow/eset/create_pdata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 c8abe63e..e86e8179 100644 --- a/target/nextflow/eset/create_pdata/main.nf +++ b/target/nextflow/eset/create_pdata/main.nf @@ -1,4 +1,4 @@ -// create_pdata v0.14.6 +// create_pdata v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3252,7 +3252,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3293,12 +3293,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/eset/create_pdata", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3812,7 +3812,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/eset/create_pdata", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/eset/create_pdata/nextflow.config b/target/nextflow/eset/create_pdata/nextflow.config index f3a333e5..41b96c3a 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 = 'v0.14.6' + version = 'v0.14.7' 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 44167746..f6682b4f 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" 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 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 ed2d246d..23bcd6d7 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 v0.14.6 +// check_eset v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "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" : "v0.14.6", + "target_tag" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3906,7 +3906,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "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 f9c618fa..225faea9 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 = 'v0.14.6' + version = 'v0.14.7' 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 a3595809..b609c376 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" 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 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 09e2459c..55aceed7 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 v0.14.6 +// check_cutadapt_output v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3213,7 +3213,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "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" : "v0.14.6" + "tag" : "v0.14.7" }, "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 f85c7177..8ba72fa3 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 = 'v0.14.6' + version = 'v0.14.7' 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 7fb8276d..915610ca 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_fastqs/_viash.yaml b/target/nextflow/io/publish_fastqs/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/io/publish_fastqs/_viash.yaml +++ b/target/nextflow/io/publish_fastqs/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 aa6f08b5..183bf2ff 100644 --- a/target/nextflow/io/publish_fastqs/main.nf +++ b/target/nextflow/io/publish_fastqs/main.nf @@ -1,4 +1,4 @@ -// publish_fastqs v0.14.6 +// publish_fastqs v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "argument_groups" : [ { "name" : "Input arguments", @@ -3184,7 +3184,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3207,12 +3207,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_fastqs", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3682,7 +3682,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_fastqs", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_fastqs/nextflow.config b/target/nextflow/io/publish_fastqs/nextflow.config index 336b5622..d0f581ca 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 = 'v0.14.6' + version = 'v0.14.7' 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 8081408c..ae88fc21 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: "v0.14.6" +version: "v0.14.7" argument_groups: - name: "Input arguments" arguments: @@ -77,6 +77,15 @@ argument_groups: direction: "input" multiple: false multiple_sep: ";" + - type: "file" + name: "--run_metadata" + info: null + must_exist: true + create_parent: true + required: true + direction: "input" + multiple: false + multiple_sep: ";" - name: "Output directory" description: "Determines the name of output directories\n" arguments: @@ -158,6 +167,15 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--run_metadata_output" + info: null + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--html_report_output" info: null @@ -261,7 +279,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.6" + target_tag: "v0.14.7" namespace_separator: "/" setup: - type: "apt" @@ -279,11 +297,11 @@ build_info: output: "target/nextflow/io/publish_results" executable: "target/nextflow/io/publish_results/main.nf" viash_version: "0.9.4" - git_commit: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 +333,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/io/publish_results/_viash.yaml b/target/nextflow/io/publish_results/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/io/publish_results/_viash.yaml +++ b/target/nextflow/io/publish_results/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 42539cf4..550abde9 100644 --- a/target/nextflow/io/publish_results/main.nf +++ b/target/nextflow/io/publish_results/main.nf @@ -1,4 +1,4 @@ -// publish_results v0.14.6 +// publish_results v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "argument_groups" : [ { "name" : "Input arguments", @@ -3117,6 +3117,16 @@ meta = [ "direction" : "input", "multiple" : false, "multiple_sep" : ";" + }, + { + "type" : "file", + "name" : "--run_metadata", + "must_exist" : true, + "create_parent" : true, + "required" : true, + "direction" : "input", + "multiple" : false, + "multiple_sep" : ";" } ] }, @@ -3218,6 +3228,16 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "file", + "name" : "--run_metadata_output", + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--html_report_output", @@ -3346,7 +3366,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3369,12 +3389,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish_results", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 +3412,7 @@ 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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3433,6 +3453,7 @@ $( if [ ! -z ${VIASH_PAR_F_DATA+x} ]; then echo "${VIASH_PAR_F_DATA}" | sed "s#' $( if [ ! -z ${VIASH_PAR_P_DATA+x} ]; then echo "${VIASH_PAR_P_DATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data='&'#" ; else echo "# par_p_data="; fi ) $( if [ ! -z ${VIASH_PAR_HTML_REPORT+x} ]; then echo "${VIASH_PAR_HTML_REPORT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report='&'#" ; else echo "# par_html_report="; fi ) $( if [ ! -z ${VIASH_PAR_RUN_PARAMS+x} ]; then echo "${VIASH_PAR_RUN_PARAMS}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params='&'#" ; else echo "# par_run_params="; fi ) +$( if [ ! -z ${VIASH_PAR_RUN_METADATA+x} ]; then echo "${VIASH_PAR_RUN_METADATA}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_metadata='&'#" ; else echo "# par_run_metadata="; fi ) $( if [ ! -z ${VIASH_PAR_STAR_OUTPUT_DIR+x} ]; then echo "${VIASH_PAR_STAR_OUTPUT_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_output_dir='&'#" ; else echo "# par_star_output_dir="; fi ) $( if [ ! -z ${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR+x} ]; then echo "${VIASH_PAR_NRREADSNRGENESPERCHROM_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_nrReadsNrGenesPerChrom_dir='&'#" ; else echo "# par_nrReadsNrGenesPerChrom_dir="; fi ) $( if [ ! -z ${VIASH_PAR_STAR_QC_METRICS_DIR+x} ]; then echo "${VIASH_PAR_STAR_QC_METRICS_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_star_qc_metrics_dir='&'#" ; else echo "# par_star_qc_metrics_dir="; fi ) @@ -3440,6 +3461,7 @@ $( if [ ! -z ${VIASH_PAR_ESET_DIR+x} ]; then echo "${VIASH_PAR_ESET_DIR}" | sed $( if [ ! -z ${VIASH_PAR_F_DATA_DIR+x} ]; then echo "${VIASH_PAR_F_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_f_data_dir='&'#" ; else echo "# par_f_data_dir="; fi ) $( if [ ! -z ${VIASH_PAR_P_DATA_DIR+x} ]; then echo "${VIASH_PAR_P_DATA_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_p_data_dir='&'#" ; else echo "# par_p_data_dir="; fi ) $( if [ ! -z ${VIASH_PAR_RUN_PARAMS_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_PARAMS_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_params_output='&'#" ; else echo "# par_run_params_output="; fi ) +$( if [ ! -z ${VIASH_PAR_RUN_METADATA_OUTPUT+x} ]; then echo "${VIASH_PAR_RUN_METADATA_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_run_metadata_output='&'#" ; else echo "# par_run_metadata_output="; fi ) $( if [ ! -z ${VIASH_PAR_HTML_REPORT_OUTPUT+x} ]; then echo "${VIASH_PAR_HTML_REPORT_OUTPUT}" | sed "s#'#'\\"'\\"'#g;s#.*#par_html_report_output='&'#" ; else echo "# par_html_report_output="; fi ) $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi ) $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\\"'\\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi ) @@ -3482,6 +3504,7 @@ declare -A path_pars_dirs=( declare -A path_pars_files=( ["par_html_report_output"]="par_html_report" ["par_run_params_output"]="par_run_params" + ["par_run_metadata_output"]="par_run_metadata" ) echo "Canonicalizing output paths." @@ -3909,7 +3932,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/io/publish_results", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish_results/nextflow.config b/target/nextflow/io/publish_results/nextflow.config index 4e2cf4a1..30217082 100644 --- a/target/nextflow/io/publish_results/nextflow.config +++ b/target/nextflow/io/publish_results/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish_results' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.14.6' + version = 'v0.14.7' description = 'Publish the results' } diff --git a/target/nextflow/io/publish_results/nextflow_schema.json b/target/nextflow/io/publish_results/nextflow_schema.json index b83eb8e6..eb4ca039 100644 --- a/target/nextflow/io/publish_results/nextflow_schema.json +++ b/target/nextflow/io/publish_results/nextflow_schema.json @@ -82,6 +82,13 @@ "exists": true, "description": "", "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " + }, + "run_metadata": { + "type": "string", + "format": "path", + "exists": true, + "description": "", + "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. " } } }, @@ -146,6 +153,13 @@ "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_params_output\"`, direction: `output`. ", "default": "$id.$key.run_params_output" }, + "run_metadata_output": { + "type": "string", + "format": "path", + "description": "", + "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.run_metadata_output\"`, direction: `output`. ", + "default": "$id.$key.run_metadata_output" + }, "html_report_output": { "type": "string", "format": "path", diff --git a/target/nextflow/parallel_map/.config.vsh.yaml b/target/nextflow/parallel_map/.config.vsh.yaml index 84489db3..b7d5c4bc 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: "v0.14.6" +version: "v0.14.7" authors: - name: "Dries Schaumont" roles: @@ -248,7 +248,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/parallel_map/_viash.yaml b/target/nextflow/parallel_map/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/parallel_map/_viash.yaml +++ b/target/nextflow/parallel_map/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 5bd1bba9..ffb9bdaf 100644 --- a/target/nextflow/parallel_map/main.nf +++ b/target/nextflow/parallel_map/main.nf @@ -1,4 +1,4 @@ -// parallel_map v0.14.6 +// parallel_map v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3332,7 +3332,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3379,12 +3379,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/parallel_map", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -4173,7 +4173,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/parallel_map", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/parallel_map/nextflow.config b/target/nextflow/parallel_map/nextflow.config index 33c405fd..ad3ae925 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 = 'v0.14.6' + version = 'v0.14.7' 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 9d7f4d39..07fd7864 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/report/create_report/_viash.yaml b/target/nextflow/report/create_report/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/report/create_report/_viash.yaml +++ b/target/nextflow/report/create_report/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 ecba491a..d37effb9 100644 --- a/target/nextflow/report/create_report/main.nf +++ b/target/nextflow/report/create_report/main.nf @@ -1,4 +1,4 @@ -// create_report v0.14.6 +// create_report v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3261,7 +3261,7 @@ meta = [ "id" : "docker", "image" : "rocker/r2u:24.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3334,12 +3334,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/report/create_report", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3849,7 +3849,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/report/create_report", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/report/create_report/nextflow.config b/target/nextflow/report/create_report/nextflow.config index 4b9fd2b9..640f9712 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 = 'v0.14.6' + version = 'v0.14.7' 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 1e0da0c1..b02983c8 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/combine_star_logs/_viash.yaml b/target/nextflow/stats/combine_star_logs/_viash.yaml index 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 99bef693..151c33a4 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 v0.14.6 +// combine_star_logs v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3254,7 +3254,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3977,7 +3977,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/combine_star_logs", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/combine_star_logs/nextflow.config b/target/nextflow/stats/combine_star_logs/nextflow.config index 76b269c6..801e62c4 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 = 'v0.14.6' + version = 'v0.14.7' 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 2f10e487..5ca3b008 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_pool_statistics/_viash.yaml b/target/nextflow/stats/generate_pool_statistics/_viash.yaml index 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 7f48e20f..4370d378 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 v0.14.6 +// generate_pool_statistics v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3238,7 +3238,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3832,7 +3832,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_pool_statistics", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_pool_statistics/nextflow.config b/target/nextflow/stats/generate_pool_statistics/nextflow.config index 66c148b9..f35d2363 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 = 'v0.14.6' + version = 'v0.14.7' 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 aa3169fe..f3b76980 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: "v0.14.6" +version: "v0.14.7" 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: "v0.14.6" + target_tag: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/stats/generate_well_statistics/_viash.yaml b/target/nextflow/stats/generate_well_statistics/_viash.yaml index 7758cabb..e4186d40 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: v0.14.6 +version: v0.14.7 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 e0ea51bd..a7d51f7e 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 v0.14.6 +// generate_well_statistics v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3319,7 +3319,7 @@ meta = [ "id" : "docker", "image" : "python:3.13-trixie", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3905,7 +3905,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/stats/generate_well_statistics", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stats/generate_well_statistics/nextflow.config b/target/nextflow/stats/generate_well_statistics/nextflow.config index c937beb5..a6755008 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 = 'v0.14.6' + version = 'v0.14.7' 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 dcee1e58..a435e259 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: "v0.14.6" +version: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" 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: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/concatRuns/_viash.yaml b/target/nextflow/utils/concatRuns/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/utils/concatRuns/_viash.yaml +++ b/target/nextflow/utils/concatRuns/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 c756afc1..60769e2d 100644 --- a/target/nextflow/utils/concatRuns/main.nf +++ b/target/nextflow/utils/concatRuns/main.nf @@ -1,4 +1,4 @@ -// concatRuns v0.14.6 +// concatRuns v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "argument_groups" : [ { "name" : "Arguments", @@ -3229,12 +3229,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/utils/concatRuns", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/utils/concatRuns/nextflow.config b/target/nextflow/utils/concatRuns/nextflow.config index 29a7cdeb..4f2c62c8 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 = 'v0.14.6' + version = 'v0.14.7' 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 e22d535d..38b4b1b7 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: "v0.14.6" +version: "v0.14.7" argument_groups: - name: "Inputs" arguments: @@ -20,23 +20,14 @@ 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 - default: - - "params.yaml" + example: + - "output.yaml" must_exist: true create_parent: true required: true @@ -137,7 +128,7 @@ engines: id: "docker" image: "python:3.12-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.14.6" + target_tag: "v0.14.7" namespace_separator: "/" setup: - type: "apt" @@ -160,11 +151,11 @@ build_info: output: "target/nextflow/utils/save_params" executable: "target/nextflow/utils/save_params/main.nf" viash_version: "0.9.4" - git_commit: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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\ @@ -196,7 +187,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/utils/save_params/_viash.yaml b/target/nextflow/utils/save_params/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/utils/save_params/_viash.yaml +++ b/target/nextflow/utils/save_params/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 ce392cb4..9bcfddcd 100644 --- a/target/nextflow/utils/save_params/main.nf +++ b/target/nextflow/utils/save_params/main.nf @@ -1,4 +1,4 @@ -// save_params v0.14.6 +// save_params v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "argument_groups" : [ { "name" : "Inputs", @@ -3054,15 +3054,6 @@ 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" : ";" } ] }, @@ -3073,8 +3064,8 @@ meta = [ "type" : "file", "name" : "--output", "description" : "The output YAML file\n", - "default" : [ - "params.yaml" + "example" : [ + "output.yaml" ], "must_exist" : true, "create_parent" : true, @@ -3201,7 +3192,7 @@ meta = [ "id" : "docker", "image" : "python:3.12-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.14.6", + "target_tag" : "v0.14.7", "namespace_separator" : "/", "setup" : [ { @@ -3232,12 +3223,12 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/utils/save_params", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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" : { @@ -3255,7 +3246,7 @@ 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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3295,7 +3286,6 @@ 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 = { @@ -3324,18 +3314,10 @@ 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') @@ -3345,26 +3327,8 @@ 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(output_data, f, default_flow_style=False, Dumper=Dumper) + yaml.dump(params, f, default_flow_style=False, Dumper=Dumper) VIASHMAIN python -B "$tempscript" ''' @@ -3747,7 +3711,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/htrnaseq/utils/save_params", - "tag" : "v0.14.6" + "tag" : "v0.14.7" }, "tag" : "$id" }'''), diff --git a/target/nextflow/utils/save_params/nextflow.config b/target/nextflow/utils/save_params/nextflow.config index 83423f42..07acbfe7 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 = 'v0.14.6' + version = 'v0.14.7' 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 6aa7a23b..d6f579fc 100644 --- a/target/nextflow/utils/save_params/nextflow_schema.json +++ b/target/nextflow/utils/save_params/nextflow_schema.json @@ -18,11 +18,6 @@ "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`. " } } }, @@ -35,8 +30,8 @@ "type": "string", "format": "path", "description": "The output YAML file\n", - "help_text": "Type: `file`, multiple: `False`, required, default: `\"params.yaml\"`, direction: `output`. ", - "default": "params.yaml" + "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.yaml\"`, direction: `output`, example: `\"output.yaml\"`. ", + "default": "$id.$key.output.yaml" } } }, diff --git a/target/nextflow/workflows/htrnaseq/.config.vsh.yaml b/target/nextflow/workflows/htrnaseq/.config.vsh.yaml index 8a679d32..d0373486 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: "v0.14.6" +version: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" 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: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/htrnaseq/_viash.yaml b/target/nextflow/workflows/htrnaseq/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/workflows/htrnaseq/_viash.yaml +++ b/target/nextflow/workflows/htrnaseq/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 5d469ecd..179ae148 100644 --- a/target/nextflow/workflows/htrnaseq/main.nf +++ b/target/nextflow/workflows/htrnaseq/main.nf @@ -1,4 +1,4 @@ -// htrnaseq v0.14.6 +// htrnaseq v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "authors" : [ { "name" : "Dries Schaumont", @@ -3442,12 +3442,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/htrnaseq", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/htrnaseq/nextflow.config b/target/nextflow/workflows/htrnaseq/nextflow.config index ff3194a5..32f9ac8b 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 = 'v0.14.6' + version = 'v0.14.7' author = 'Dries Schaumont' } diff --git a/target/nextflow/workflows/runner/.config.vsh.yaml b/target/nextflow/workflows/runner/.config.vsh.yaml index 41a35064..2b958ba3 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: "v0.14.6" +version: "v0.14.7" argument_groups: - name: "Input arguments" arguments: @@ -133,6 +133,19 @@ argument_groups: direction: "output" multiple: false multiple_sep: ";" + - type: "file" + name: "--run_metadata" + description: "YAML file containing meta information about the file — .e.g. versions\ + \ of (sub)-workflows.\n" + info: null + default: + - "metadata.yaml" + must_exist: true + create_parent: true + required: false + direction: "output" + multiple: false + multiple_sep: ";" - type: "file" name: "--star_output_dir" info: null @@ -337,7 +350,7 @@ build_info: output: "target/nextflow/workflows/runner" executable: "target/nextflow/workflows/runner/main.nf" viash_version: "0.9.4" - git_commit: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" dependencies: - "target/_private/nextflow/utils/listInputDir" @@ -348,7 +361,7 @@ build_info: - "target/nextflow/utils/save_params" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 +393,7 @@ package_config: \ '_viash.yaml'}\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/runner/_viash.yaml b/target/nextflow/workflows/runner/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/workflows/runner/_viash.yaml +++ b/target/nextflow/workflows/runner/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 cf40dc01..9a729237 100644 --- a/target/nextflow/workflows/runner/main.nf +++ b/target/nextflow/workflows/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.14.6 +// runner v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "argument_groups" : [ { "name" : "Input arguments", @@ -3181,6 +3181,20 @@ meta = [ "multiple" : false, "multiple_sep" : ";" }, + { + "type" : "file", + "name" : "--run_metadata", + "description" : "YAML file containing meta information about the file — .e.g. versions of (sub)-workflows.\n", + "default" : [ + "metadata.yaml" + ], + "must_exist" : true, + "create_parent" : true, + "required" : false, + "direction" : "output", + "multiple" : false, + "multiple_sep" : ";" + }, { "type" : "file", "name" : "--star_output_dir", @@ -3452,12 +3466,12 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/workflows/runner", "viash_version" : "0.9.4", - "git_commit" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 +3489,7 @@ 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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", @@ -3546,17 +3560,20 @@ def get_workflow_analysis() { } // 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 main_entry = [ + "name": meta.config.name ?: "unknown_name", + "version": meta.config.version ?: "unknown_version", + "dependencies": dependencies + ] - def analysis = [main_entry] + def analysis = ["versions": [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. */ @@ -3573,12 +3590,21 @@ workflow save_params_wf { def all_states = states.collect{it[1]} def run_params_output_templates = all_states.collect{it.run_params} assert run_params_output_templates.unique().size() == 1: "The value for the 'run_params' parameter is not the same across runs." - def new_state = ["run_params": run_params_output_templates[0], "all_states": all_states] + + def run_metadata_output_templates = all_states.collect{it.run_metadata} + assert run_metadata_output_templates.unique().size() == 1: "The value for the 'run_metadata' parameter is not the same across runs." + + def new_state = [ + "run_params": run_params_output_templates[0], + "run_metadata": run_metadata_output_templates[0], + "all_states": all_states + ] return [new_id, new_state] } | save_params.run( key: "save_params_runner", fromState: {id, state -> + def convertPaths convertPaths = { value -> if (value instanceof java.nio.file.Path) @@ -3598,21 +3624,32 @@ 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, - "workflow_analysis": encoded_analysis + "output": state.run_params + ] + }, + toState: ["run_params": "output"] + ) + | save_params.run( + key: "save_meta_runner", + fromState: {id, state -> + 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": encoded_analysis, + "output": state.run_metadata, ] }, toState: { id, output, state -> - state + [ run_params: output.output ] + state + [ run_metadata: output.output ] } ) + emit: output_ch } @@ -3811,7 +3848,8 @@ workflow run_wf { "eset_dir", "f_data_dir", "p_data_dir", - "run_params" + "run_params", + "run_metadata" ] def new_state = demux_state + input_state.subMap(keys_to_transfer) @@ -3822,7 +3860,8 @@ workflow run_wf { "eset_dir", "f_data_dir", "p_data_dir", - "run_params" + "run_params", + "run_metadata" ] new_state = new_state.collectEntries{k, v -> def newKey = keys_to_rename.contains(k) ? "${k}_workflow" : k @@ -3908,7 +3947,10 @@ workflow run_wf { // Add the run parameter YAML to the output | map {id, grouped_ch_state, _, save_params_state -> assert save_params_state.run_params.isFile() - def new_state = grouped_ch_state + ["run_params": save_params_state.run_params] + def new_state = grouped_ch_state + [ + "run_params": save_params_state.run_params, + "run_metadata": save_params_state.run_metadata + ] return [id, new_state] } // Group the events in order to publish the results per experiment @@ -3946,8 +3988,10 @@ workflow run_wf { "f_data_dir_workflow", "p_data_dir_workflow", "run_params_workflow", + "run_metadata_workflow", "f_data", - "run_params" + "run_params", + "run_metadata" ] def state_unique_keys = state_keys_unique.inject([:]) { state_to_update, argument_name -> argument_values = states.collect{it.get(argument_name)}.unique() @@ -3990,9 +4034,11 @@ workflow run_wf { p_data: state.p_data, html_report: state.html_report, run_params: state.run_params, + run_metadata: state.run_metadata, // Output locations html_report_output: "${state.results_prefix}/${state.html_report.name}", run_params_output: "${state.results_prefix}/${state.run_params_workflow}", + run_metadata_output: "${state.results_prefix}/${state.run_metadata_workflow}", star_output_dir: "${state.results_prefix}/${state.star_output_dir_workflow}", nrReadsNrGenesPerChrom_dir: "${state.results_prefix}/${state.nrReadsNrGenesPerChrom_dir_workflow}", star_qc_metrics_dir: "${state.results_prefix}/${state.star_qc_metrics_dir_workflow}", @@ -4004,6 +4050,7 @@ workflow run_wf { toState: { id, result, state -> result + [ "run_params": state.run_params, + "run_metadata": state.run_metadata, "_meta": ["join_id": state.event_id[0]], "results_prefix": state.results_prefix ] @@ -4108,6 +4155,7 @@ workflow run_wf { "f_data_dir", "p_data_dir", "run_params", + "run_metadata", "_meta" ] ) diff --git a/target/nextflow/workflows/runner/nextflow.config b/target/nextflow/workflows/runner/nextflow.config index 9435a59a..96280173 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 = 'v0.14.6' + version = 'v0.14.7' description = 'Runner for HT RNA-seq pipeline' } diff --git a/target/nextflow/workflows/runner/nextflow_schema.json b/target/nextflow/workflows/runner/nextflow_schema.json index 19d0c53c..f3899e32 100644 --- a/target/nextflow/workflows/runner/nextflow_schema.json +++ b/target/nextflow/workflows/runner/nextflow_schema.json @@ -109,6 +109,13 @@ "help_text": "Type: `file`, multiple: `False`, default: `\"params.yaml\"`, direction: `output`. ", "default": "params.yaml" }, + "run_metadata": { + "type": "string", + "format": "path", + "description": "YAML file containing meta information about the file — .e.g", + "help_text": "Type: `file`, multiple: `False`, default: `\"metadata.yaml\"`, direction: `output`. ", + "default": "metadata.yaml" + }, "star_output_dir": { "type": "string", "format": "path", diff --git a/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml b/target/nextflow/workflows/well_demultiplex/.config.vsh.yaml index 09259948..d99c52d0 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: "v0.14.6" +version: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" 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: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_demultiplex/_viash.yaml b/target/nextflow/workflows/well_demultiplex/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/workflows/well_demultiplex/_viash.yaml +++ b/target/nextflow/workflows/well_demultiplex/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 e3c579ef..973c4879 100644 --- a/target/nextflow/workflows/well_demultiplex/main.nf +++ b/target/nextflow/workflows/well_demultiplex/main.nf @@ -1,4 +1,4 @@ -// well_demultiplex v0.14.6 +// well_demultiplex v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_demultiplex/nextflow.config b/target/nextflow/workflows/well_demultiplex/nextflow.config index a1ce9d40..4687b21a 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 = 'v0.14.6' + version = 'v0.14.7' 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 eb9194f2..c5bb6508 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: "v0.14.6" +version: "v0.14.7" 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: "9346c55e3f894994935b0928759dca9e56866d37" + git_commit: "07ba686a4603dac053f3e9f9990081cdb506169e" git_remote: "https://github.com/viash-hub/htrnaseq" package_config: name: "htrnaseq" - version: "v0.14.6" + version: "v0.14.7" 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 := 'v0.14.6'" + - ".engines[.type == 'docker'].target_tag := 'v0.14.7'" keywords: - "bioinformatics" - "sequencing" diff --git a/target/nextflow/workflows/well_metadata/_viash.yaml b/target/nextflow/workflows/well_metadata/_viash.yaml index 7758cabb..e4186d40 100644 --- a/target/nextflow/workflows/well_metadata/_viash.yaml +++ b/target/nextflow/workflows/well_metadata/_viash.yaml @@ -1,5 +1,5 @@ name: htrnaseq -version: v0.14.6 +version: v0.14.7 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 f4cc4ee4..8448038d 100644 --- a/target/nextflow/workflows/well_metadata/main.nf +++ b/target/nextflow/workflows/well_metadata/main.nf @@ -1,4 +1,4 @@ -// well_metadata v0.14.6 +// well_metadata v0.14.7 // // 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" : "v0.14.6", + "version" : "v0.14.7", "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" : "9346c55e3f894994935b0928759dca9e56866d37", + "git_commit" : "07ba686a4603dac053f3e9f9990081cdb506169e", "git_remote" : "https://github.com/viash-hub/htrnaseq" }, "package_config" : { "name" : "htrnaseq", - "version" : "v0.14.6", + "version" : "v0.14.7", "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 := 'v0.14.6'" + ".engines[.type == 'docker'].target_tag := 'v0.14.7'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/workflows/well_metadata/nextflow.config b/target/nextflow/workflows/well_metadata/nextflow.config index ea192e93..45e8363b 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 = 'v0.14.6' + version = 'v0.14.7' author = 'Dries Schaumont' }