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KrakenUniq pathnames fix #604
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v1.2.3 - Bouncy Basenji Patch PR
This PR is against the
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Oops, yes I see the issue - we never considered running a single sample 😅 So yeah this is a combination of having to 'batch' KrakenUniq runs into multiple samples, and a really annoying behaviour of Java/Groovy that if you give I think this PR makes sense, will check tests once they've completed :) |
But don't forget changelog @AlexHoratio ! |
Wonderful, thank you!! 😄 I just updated the changelog. |
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I did a test to compare current -r dev -profile test
to have the expected ~6 samples, then this PR with -profile test
which gave the expected ~6 samples, and finally a samplesheet with just a single entry also with this PR and that produced one file as expected. So all good from me :)
Thank you @AlexHoratio ! |
Hi!! I can't say I completely understand how Nextflow works, but I was getting this fatal error, only running one sample in my samplesheet:
With more than one sample, I was having a "file name collision" error, probably because it was splitting at every '/' and doing that to each sample in the samplesheet.
By placing [] around reads before it gets bundled with prefixes, sorted, placed into batches, etc, it solves the pathname from breaking apart.
I'm not sure if anyone else has encountered this bug, but this has fixed the pipeline for me! I can now run KrakenUniq successfully, with either one or multiple samples.
My samplesheet looks like this:
databases.csv:
I hope this is helpful. If it's a unique (hehe) error just for me (a.k.a., if I have been doing something wrong), please let me know!!
PR checklist
nf-core pipelines lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).