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PR to fix issue 90 (Pipeline fails when test.fa missing) #92

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PR to fix issue 90 (Pipeline fails when test.fa missing) #92

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  • Removed mentions of file "test.fa", replacing with null or empty string
  • Removed schema_ignore_params argument for non-existent parameter genomes

Tested this change on real data, but recommend further review/testing before merging. Attached relevant sample sheet, command, and Nextflow log file.

nextflow_test_run_90.log
sample_sheet_test.csv
testing.sh.txt

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/bacpaq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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