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Fix nanopore fasta input being incorrectly channeled #518

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merged 4 commits into from
Sep 5, 2024
Merged

Fix nanopore fasta input being incorrectly channeled #518

merged 4 commits into from
Sep 5, 2024

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jfy133
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@jfy133 jfy133 commented Sep 3, 2024

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/taxprofiler branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@jfy133
Fix bug where Nanopore FASTA files would be picked up into the FASTQ …
37b275e 
…branch and thus not passed into the right FASTA channels
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jfy133 commented Sep 3, 2024

I wonder if we should duplciate the ILLUMINA FASTA file int he samplesheet to also have nanopore... waht do you think @nf-core/taxprofiler ?

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github-actions bot commented Sep 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 811d33a

+| ✅ 257 tests passed       |+
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-04 07:35:27

jfy133
jfy133 commented Sep 3, 2024
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LilyAnderssonLee commented Sep 3, 2024 •
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I wonder if we should duplciate the ILLUMINA FASTA file int he samplesheet to also have nanopore... waht do you think @nf-core/taxprofiler ?

I think that's a good idea. If so, should we include it in the test data in this bouncy-basen release?

LilyAnderssonLee
LilyAnderssonLee approved these changes Sep 3, 2024
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Well done! It looks good to me.

LilyAnderssonLee
LilyAnderssonLee reviewed Sep 3, 2024
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Midnighter
Midnighter reviewed Sep 3, 2024
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jfy133 commented Sep 4, 2024

I wonder if we should duplciate the ILLUMINA FASTA file int he samplesheet to also have nanopore... waht do you think @nf-core/taxprofiler ?

I think that's a good idea. If so, should we include it in the test data in this bouncy-basen release?

Yes good idea :)

@jfy133 @LilyAnderssonLee
Update CHANGELOG.md
6149c42 
Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com>
jfy133
jfy133 commented Sep 4, 2024
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I wonder if we should duplciate the ILLUMINA FASTA file int he samplesheet to also have nanopore... waht do you think @nf-core/taxprofiler ?

I think that's a good idea. If so, should we include it in the test data in this bouncy-basen release?

Yes good idea :)

I will update test samplesheet

@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Sep 5, 2024
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@LilyAnderssonLee LilyAnderssonLee merged commit 5e0d556 into dev Sep 5, 2024
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@LilyAnderssonLee LilyAnderssonLee deleted the fix-nanopore-fasta branch September 5, 2024 07:45
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@LilyAnderssonLee LilyAnderssonLee LilyAnderssonLee approved these changes

@Midnighter Midnighter Midnighter left review comments

@sofstam sofstam sofstam approved these changes

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