Add rgi/bwt #9873
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Add rgi/bwt #9873
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- Use template from rgi/main
- Use fastq pair instead of single fasta file
- 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)
- Use '--local' flag as default
- Code review from nf-core#9585
- Create topics field in meta.yml
Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
- capture topics appropriately in meta.yml
- Remove whitespace
- Fix escape character in versions output
SPPearce
reviewed
Feb 4, 2026
Code review for nf-core#9873 Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
Merge branch 'rgi/bwt' of github.com:vinisalazar/modules into rgi/bwt
SPPearce
reviewed
Feb 5, 2026
| script "modules/nf-core/untar/main.nf" | ||
| process { | ||
| """ | ||
| file('https://card.mcmaster.ca/latest/data', checkIfExists: true).copyTo('card-data.tar.bz2') |
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We don't like to use externally hosted files, as they can sometimes become missing over time. How big is this?
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@SPPearce thanks again for the review. The file is 4.5 Mb. What would be the best practice in this case?
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Best practice will be to make a PR into the test-datasets repository then.
Could you make it any smaller than that?
That is quite annoyingly finnicky (and redoing how we do test-datasets has been on the to-do list for a long time now).
- Make the file smaller if possible, but still let the tool run.
- Shallow clone nf-core/test-datasets, just the modules branch.
- Make a PR adding the file into an appropriate place. Please don't put it in
delete_me, find somewhere more appropriate. - Once the PR is in, you can refer to the file like the others in the test.
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Thanks @SPPearce. PR created, see below.
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
vinisalazar
added a commit
to vinisalazar/test-datasets
that referenced
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Feb 9, 2026
Data for testing the rgi modules. See nf-core/modules#9873 for discussion.
vinisalazar
added a commit
to vinisalazar/test-datasets
that referenced
this pull request
Feb 11, 2026
Data for testing the rgi modules. See nf-core/modules#9873 for discussion.
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Summary of changes:
This PR is a follow-up of #9585. See that for discussion.
PR checklist
Closes #XXX
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda