feat: add vcontact3/run module#12198
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we don't use this file anymore 🙂
mashehu
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mashehu
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it looks like you started this module an outdated template, so I would recommend to rerun nf-core moduels create with nf-core/tools version 4.0.2. (and then copy over the code)
mashehu
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mashehu
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looks like you missed the template changes iin the main.nf 🙂
| cat > versions.yml <<-EOF_VERSIONS | ||
| "${task.process}": | ||
| vcontact3: \$( vcontact3 --version 2>&1 | grep -oP 'vcontact3, version \\K[^\\s]+' ) | ||
| EOF_VERSIONS |
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use version topics please https://nf-co.re/docs/tutorials/migrate_to_topics/update_modules
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
| tag "vcontact3" | ||
| tag "vcontact3/run" | ||
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| test("vcontact3_run - stub") { |
| - vcontact3_output/: | ||
| type: directory | ||
| description: VCONTACT3 output directory containing clustering results | ||
| pattern: "vcontact3_output/" |
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you also need to add the versions_vcontact3 channel here.
This should be automatically resolved withnf-core modules lint --fix
…versions_vcontact3 output
…ntact3 output, snapshot
| touch vcontact3_output/clusters.csv | ||
| touch vcontact3_output/merged_df.csv |
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based on this, the output section should capture the csv files, not the whole directory
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are you writing the snapshots by hand? they don't follow the nf-test format. you can generate them using |
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Description
Implements the VCONTACT3/RUN module for viral genome clustering using protein-level homology comparison.
Related Issues
Closes #11569
Module Details
Checklist
Testing
Module created with proper Nextflow DSL2 structure. Ready for integration testing with nf-core CI/CD pipeline.