Update provenance format #27
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This is looking great. Could you add a section to the README that describes the format of the provenance file? See the kma-cgmlst README for an example. Please be sure not to include any real sample IDs in the example (just replace with https://github.com/BCCDC-PHL/kma-cgmlst?tab=readme-ov-file#provenance |
dfornika
requested changes
Feb 7, 2024
…f into update-provenance update remote
dfornika
approved these changes
Feb 8, 2024
modules/tbprofiler.nf
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| printf -- "- process_name: tbprofiler\\n" > ${sample_id}_tbprofiler_provenance.yml | ||
| printf -- " tools:\\n" >> ${sample_id}_tbprofiler_provenance.yml | ||
| printf -- " - tool_name: tb-profiler\\n" >> ${sample_id}_tbprofiler_provenance.yml | ||
| printf -- " database_version: \$(grep 'Database version' ${sample_id}_tbprofiler_full_report.csv | cut -d',' -f2)\\n" >> ${sample_id}_tbprofiler_provenance.yml |
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Can we remove this database_version attribute here? That's important provenance info but I think we may need to find another place to put it. It doesn't fit there in the schema.
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...nevermind, I've done it myself.
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Fixes #20
Adding provenance in the same format as BCCDC-PHL/kma-cgmlst
Format may still be adjusted to add name and and flag and optional description variable.
TBD: BCCDC-PHL/pipeline-provenance-schema