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Summary of changes:

  • rgi/bwt: add draft
  • rgi/bwt: editing input channel

cc @nickp60

  - Use template from rgi/main
  - Use fastq pair instead of single fasta file
@vinisalazar vinisalazar marked this pull request as draft December 18, 2025 01:31
  - add fastq extensions to 'pattern'
  - Trying to pass linter
  - build KMA/BWT index in workdir instead of program executable dir
  - update test snapshot
  - Don't check temp/ directory on snapshot, is different every time
  - Update snapshot
  - provide input.reads as list
  - don't check tsv snapshot (it's different every time)
  - json files are in random order so snapshot differs every time (I think)
@vinisalazar vinisalazar marked this pull request as ready for review December 18, 2025 06:08
@vinisalazar
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@nickp60 we might want to adjust the output channels a little bit, looks to me as though these are the main files:

test.allele_mapping_data.txt
test.artifacts_mapping_stats.txt
test.gene_mapping_data.txt
test.overall_mapping_stats.txt
test.reference_mapping_stats.txt

@vinisalazar
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@SPPearce thank you for the review, addressed your comments.

  - Use '--local' flag as default
@nickp60
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nickp60 commented Dec 31, 2025

@vinisalazar Thanks for doing all this! I agree with changing the output to specify those 5 outputs; that seems in line with the description in the docs

@vinisalazar
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@SPPearce could this be merged as is, and I can have a go at @nickp60's suggestion on a later PR (along with updates to rgi/main, perhaps)?

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3 participants