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Update modules #512

Merged
merged 32 commits into from
Sep 9, 2024
Merged

Update modules #512

merged 32 commits into from
Sep 9, 2024

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LilyAnderssonLee
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Close #403

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).

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github-actions bot commented Aug 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit df25a1b

+| ✅ 268 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • 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 2024-09-07 20:35:45

@jfy133
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jfy133 commented Aug 8, 2024

To summarise the issue:

  • DIAMOND doesn't actually accept paired end input (Silent fail in taxprofiler <= 1.1.8, it would just take the first file)
  • A new check in the module expects a single file not a list, but we sometimes send pairs, and so get.Extesion() doesn't work if there is >= 1 file
  • With nopreprocessing there is no read-merging, so remains as pairs rather than a single file

@LilyAnderssonLee and my current thinking:

  • Have a warning that if paried-end data is input + diamond turned on, give a warning it will be filtered out
  • Filter out paire-dend data before it goes into diamond

@LilyAnderssonLee
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LilyAnderssonLee commented Aug 28, 2024 •
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ganon_log.zip
@jfy133 The multiqc module has been updated to the latest version, but ganon still can't be included in the MultiQC report because the log file generated by the latest ganon version 2.0.0 differs from the one generated by version 1.5.1 used in the MultiQC ganon module.

@LilyAnderssonLee
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LilyAnderssonLee commented Aug 30, 2024 •
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nanoq has been added to the MultiQC report.
multiqc_report.html.zip

@LilyAnderssonLee
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All modules have been updated except for motus/profile. I have opened a PR to update this module. But there are some issues running nf-test at the global setup MOTUS_DOWNLOADDB due to the large database. I believe we need to prepare a smaller test database for motus, which will take some time. Since Sofia is updating motus/profile for long reads, I’m considering if we could skip the update for motus/profile for now and include it in the third release. This way, we could proceed with the release this week. What do you think @nf-core/taxprofiler ?

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jfy133 commented Sep 4, 2024 •
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I had one last idea for motus/profile, so testing that otherwise yes we can skip that one for now

Update: appears to be working now, just an MD5 checksum difference for conda for some reason

@LilyAnderssonLee
Merge pull request nf-core#518 from nf-core/fix-nanopore-fasta
5e0d556 
Fix nanopore fasta input being incorrectly channeled
sofstam
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Shall it be documented in the usage that Nanoq is going to be the default option if a user chooses filtering?

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LilyAnderssonLee and others added 2 commits September 6, 2024 14:16
@LilyAnderssonLee @sofstam
Update CHANGELOG.md
ef5db33 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
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Update CHANGELOG.md
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jfy133 commented Sep 6, 2024

@LilyAnderssonLee I think we want unique file names for ALL types of files (fastq/fasta) etc!

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jfy133 commented Sep 6, 2024

@nf-core-bot fix linting

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LilyAnderssonLee commented Sep 7, 2024 •
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@LilyAnderssonLee I think we want unique file names for ALL types of files (fastq/fasta) etc!

Initially, I thought it wasn't necessary since, for FASTQ files, the reads channel from preprocessing or host removal is defined as ${meta.id}_${meta.run_accession} which is unique. But if someone wants to run profiling directly that could be a problem. I suppose I could add unique:true to the FASTQ files.

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jfy133 commented Sep 8, 2024

Initially, I thought it wasn't necessary since, for FASTQ files, the reads channel from preprocessing or host removal is defined as ${meta.id}_${meta.run_accession} which is unique. But if someone wants to run profiling directly that could be a problem. I suppose I could add unique:true to the FASTQ files.

You're right it's not so bad after the first couple of steps as indeed we come up with our own names.

But for the initial steps it might be safer, and also (now I think about it) , it would help prevent any copy pasting errors when creating the samplesheet too so I think it would be worth it :).

If someone has the exact same file name for different samples or libraries on their system, this is dangerous for them too so we can nudge them to also be more careful with that 😬

@sofstam sofstam self-requested a review September 9, 2024 08:18
@LilyAnderssonLee LilyAnderssonLee merged commit c6dfb84 into nf-core:bouncy-basenji Sep 9, 2024
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@LilyAnderssonLee LilyAnderssonLee mentioned this pull request Sep 11, 2024
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@LilyAnderssonLee @jfy133 @sofstam