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added seqfu stats #56

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@ctuni ctuni commented Oct 29, 2024 •
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Added SeqFu stats module

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/seqinspector branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
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  • 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 Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e3117f6

+| ✅ 191 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
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❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-10-30 10:27:32

@ctuni ctuni linked an issue Oct 29, 2024 that may be closed by this pull request
add SeqFu to Seqinspector #39
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MatthiasZepper
MatthiasZepper requested changes Oct 29, 2024
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Thank you for your contribution!

Ultimately, the pipeline will allow to flexibly choose the tools that are run, so having more tools in the pipeline is always great, but what exactly was your rationale here?

Admittedly, I just skimmed over the description, but to me, it seems that it is predominantly meant to run on FASTA files and for judging the quality of genome assemblies. Unless I missed some relevant arguments, its application on sequencing reads is in my opinion does not really yield too many meaningful statistics (at least for Illumina, for Nanopore probably yes)

Do you happen to have a Nanopore example? For Illumina, this is basically all you get:

┌──────────────────────────┬──────────┬────────────┬───────┬─────┬─────┬─────┬───────┬─────┬─────┐
│ File                     │ #Seq     │ Total bp   │ Avg   │ N50 │ N75 │ N90 │ auN   │ Min │ Max │
├──────────────────────────┼──────────┼────────────┼───────┼─────┼─────┼─────┼───────┼─────┼─────┤
│ S11_L001_R1_001.fastq.gz │ 35875355 │ 5417178605 │ 151.0 │ 151 │ 151 │ 151 │ 0.000 │ 151 │ 151 │
│ S11_L001_I1_001.fastq.gz │ 35875355 │ 322878195  │ 9.0   │ 9   │ 9   │ 9   │ 0.000 │ 9   │ 9   │
│ S11_L001_R2_001.fastq.gz │ 35875355 │ 5417178605 │ 151.0 │ 151 │ 151 │ 151 │ 0.000 │ 151 │ 151 │
└──────────────────────────┴──────────┴────────────┴───────┴─────┴─────┴─────┴───────┴─────┴─────┘

But with regard to the code, this already looks very good and tidy!

I am only missing a config for the module with a publishDir directive, so that the reports from the stats output channel are published in a subfolder of the outdir. Furthermore, there are possibly relevant ext.args that I overlooked and that you used for the reads?

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ctuni commented Oct 30, 2024

Thank you for your contribution!

Ultimately, the pipeline will allow to flexibly choose the tools that are run, so having more tools in the pipeline is always great, but what exactly was your rationale here?

Admittedly, I just skimmed over the description, but to me, it seems that it is predominantly meant to run on FASTA files and for judging the quality of genome assemblies. Unless I missed some relevant arguments, its application on sequencing reads is in my opinion does not really yield too many meaningful statistics (at least for Illumina, for Nanopore probably yes)

Do you happen to have a Nanopore example? For Illumina, this is basically all you get:

┌──────────────────────────┬──────────┬────────────┬───────┬─────┬─────┬─────┬───────┬─────┬─────┐
│ File                     │ #Seq     │ Total bp   │ Avg   │ N50 │ N75 │ N90 │ auN   │ Min │ Max │
├──────────────────────────┼──────────┼────────────┼───────┼─────┼─────┼─────┼───────┼─────┼─────┤
│ S11_L001_R1_001.fastq.gz │ 35875355 │ 5417178605 │ 151.0 │ 151 │ 151 │ 151 │ 0.000 │ 151 │ 151 │
│ S11_L001_I1_001.fastq.gz │ 35875355 │ 322878195  │ 9.0   │ 9   │ 9   │ 9   │ 0.000 │ 9   │ 9   │
│ S11_L001_R2_001.fastq.gz │ 35875355 │ 5417178605 │ 151.0 │ 151 │ 151 │ 151 │ 0.000 │ 151 │ 151 │
└──────────────────────────┴──────────┴────────────┴───────┴─────┴─────┴─────┴───────┴─────┴─────┘

But with regard to the code, this already looks very good and tidy!

I am only missing a config for the module with a publishDir directive, so that the reports from the stats output channel are published in a subfolder of the outdir. Furthermore, there are possibly relevant ext.args that I overlooked and that you used for the reads?

Hi @MatthiasZepper, thank you for your comments!

To be fair, I took up this issue/PR to "prepare" the pipeline with as many new modules as possible. I agree that this tool is more useful with Nanopore reads. Maybe this PR can be "frozen" until the seqinspector pipeline has a workflow for Nanopore/long read methods. Or until the pipeline accepts files that are not FASTQ (FASTA, BAM, BED, etc). Unfortunately, I don't have a Nanopore example, I'll see if there is some nanopore dataset on the test-datasets repo so I can see what the stats look like.

I'll add now the config for the publishDir and check which ext.args might be useful to add by default!

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add SeqFu to Seqinspector
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