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* Update provenance, and indenting * Fix provenance output * Remove versioned_outdir * Remove versioned_outdir
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| #!/usr/bin/env python3 | ||
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| import argparse | ||
| import json | ||
| import os | ||
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| import yaml | ||
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| def main(args): | ||
| db_metadata_path = os.path.join(args.db, 'metadata.json') | ||
| db_metadata = {} | ||
| if os.path.exists(db_metadata_path): | ||
| with open(db_metadata_path, 'r') as f: | ||
| db_metadata = json.load(f) | ||
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| if not db_metadata: | ||
| exit() | ||
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| provenance = {} | ||
| if args.provenance: | ||
| with open(args.provenance, 'r') as f: | ||
| provenance = yaml.safe_load(f) | ||
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| database_provenance = {} | ||
| database_name = db_metadata.get('dbname', None) | ||
| if database_name: | ||
| database_provenance['database_name'] = database_name | ||
| database_version = db_metadata.get('version', None) | ||
| if database_version: | ||
| database_provenance['database_version'] = database_version | ||
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| for provenance_record in provenance: | ||
| if provenance_record.get('process_name') == 'kraken2': | ||
| provenance_record['databases'] = [] | ||
| provenance_record['databases'].append(database_provenance) | ||
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| with open(args.provenance, 'w') as f: | ||
| yaml.dump(provenance, f) | ||
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| if __name__ == '__main__': | ||
| parser = argparse.ArgumentParser(description='Get metadata from Kraken database') | ||
| parser.add_argument('--provenance', help='Path to provenance file') | ||
| parser.add_argument('--db', help='Path to Kraken database') | ||
| args = parser.parse_args() | ||
| main(args) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,37 +1,41 @@ | ||
| process collect_provenance { | ||
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| tag { sample_id } | ||
| tag { sample_id } | ||
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| executor 'local' | ||
| executor 'local' | ||
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| publishDir params.versioned_outdir ? "${params.outdir}/${sample_id}/${params.pipeline_short_name}-v${params.pipeline_minor_version}-output" : "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy' | ||
| publishDir "${params.outdir}/${sample_id}", pattern: "${sample_id}_*_provenance.yml", mode: 'copy' | ||
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| input: | ||
| tuple val(sample_id), path(provenance_files) | ||
| input: | ||
| tuple val(sample_id), path(provenance_files) | ||
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| output: | ||
| tuple val(sample_id), file("${sample_id}_*_provenance.yml") | ||
| output: | ||
| tuple val(sample_id), file("${sample_id}_*_provenance.yml") | ||
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| script: | ||
| """ | ||
| cat ${provenance_files} > ${sample_id}_\$(date +%Y%m%d%H%M%S)_provenance.yml | ||
| """ | ||
| script: | ||
| """ | ||
| cat ${provenance_files} > ${sample_id}_\$(date +%Y%m%d%H%M%S)_provenance.yml | ||
| """ | ||
| } | ||
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| process pipeline_provenance { | ||
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| tag { pipeline_name + " / " + pipeline_version } | ||
| tag { pipeline_name + " / " + pipeline_version } | ||
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| executor 'local' | ||
| executor 'local' | ||
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| input: | ||
| tuple val(pipeline_name), val(pipeline_version), val(analysis_start) | ||
| input: | ||
| tuple val(session_id), val(run_name), val(pipeline_name), val(pipeline_version), val(timestamp_analysis_start) | ||
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| output: | ||
| file("pipeline_provenance.yml") | ||
| output: | ||
| file("pipeline_provenance.yml") | ||
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| script: | ||
| """ | ||
| printf -- "- pipeline_name: ${pipeline_name}\\n pipeline_version: ${pipeline_version}\\n- timestamp_analysis_start: ${analysis_start}\\n" > pipeline_provenance.yml | ||
| """ | ||
| script: | ||
| """ | ||
| printf -- "- pipeline_name: ${pipeline_name}\\n" >> pipeline_provenance.yml | ||
| printf -- " pipeline_version: ${pipeline_version}\\n" >> pipeline_provenance.yml | ||
| printf -- " nextflow_session_id: ${session_id}\\n" >> pipeline_provenance.yml | ||
| printf -- " nextflow_run_name: ${run_name}\\n" >> pipeline_provenance.yml | ||
| printf -- " timestamp_analysis_start: ${timestamp_analysis_start}\\n" >> pipeline_provenance.yml | ||
| """ | ||
| } |
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