Bracken output report addition #379
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jfy133
reviewed
Sep 20, 2023
conf/modules.config
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| [ | ||
| path: { "${params.outdir}/bracken/${meta.db_name}/" }, | ||
| mode: params.publish_dir_mode, | ||
| pattern: '*bracken.kraken2.report_bracken*.txt' |
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It's is not worth making it optional with a flag, it would be more concise to just update the glob in the tsv output e.g. with an OR statement
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Aha! I wasn't aware that was possible. Is the syntax simply pattern: 'x' OR 'y'?
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I guess perhaps you mean '*{txt,tsv}'?
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Made changes to the |
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Midnighter
reviewed
Sep 21, 2023
conf/modules.config
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| mode: params.publish_dir_mode, | ||
| pattern: '*bracken.kraken2.report_bracken*.txt' | ||
| ] | ||
| pattern: '*{.tsv,.report_bracken_species.txt}' |
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Is the .report_bracken_species infix really necessary? What if the pattern is only *.{txt,tsv}?
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It is necessary, as the report from Kraken2 (the uncorrected one) also has the .txt suffix
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Nextflow already knows not to pick up input files :), so actually txt,tsv shoudl be sufficient
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Ah that is great! Learn something new every day!
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Maybe something like?
pattern: '*{.tsv, txt}'
jfy133
requested changes
Sep 21, 2023
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I just did a test, and it's not working.
I realise now is that is because Nextflow doesn't list teh 'corrected' kraken report in it's output channels
This will require a PR to the nf-core/moduels repo to add the txt, and then once that's merged in, this PR will need up update the module in the PR in addition to the modules glob.
Sorry this is a bit more involved @hkaspersen ! But hopefully good practise :)
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No worries, there is no rush! |
updated bracken module
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Thanks for adding this @hkaspersen There is a conflict in |
…profiler into bracken_output_report_fix
jfy133
reviewed
Oct 1, 2023
jfy133
reviewed
Oct 1, 2023
jfy133
approved these changes
Oct 1, 2023
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Made a couple more very minor changes (mainly adding the file to the output docs), but otherwise I think we are GTG now! Thank you very much @hkaspersen, we look forward to further contributions from you 😉 !!!
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).I added the corrected kraken2 report from Bracken as output, as it was missing from the Bracken output. This file is used for downstream analyses of the corrected counts for each taxa, and it would be very nice to add this as output.