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feat add fastp #457

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Merged
merged 8 commits into from
Dec 19, 2023
Merged

feat add fastp #457

merged 8 commits into from
Dec 19, 2023

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@Lucpen
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@Lucpen Lucpen commented Dec 18, 2023

PR checklist

  • Added fastp to perform trimming
  • 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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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 Dec 18, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4be3219

+| ✅ 151 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-18 19:40:49

@Lucpen
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Lucpen commented Dec 18, 2023

According to what it says here the polyG should happen automatically:
# polyG tail trimming, useful for NextSeq/NovaSeq data -g, --trim_poly_g force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data

@Lucpen Lucpen requested a review from jemten December 18, 2023 15:47
@Lucpen Lucpen added the ready for review PR is ready for review label Dec 18, 2023
@Lucpen Lucpen linked an issue Dec 18, 2023 that may be closed by this pull request
Add optional trimming of fastq files #455
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jemten
jemten reviewed Dec 18, 2023
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Fast work with fastp 🚀 🥁
Comment about channel renaming, but I'm not aware of what's best practice here.

Could you add the FASTP.out.json file from the workflow to the multiqc channel?

Lucpen
Lucpen commented Dec 18, 2023
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@Lucpen Lucpen requested a review from jemten December 19, 2023 06:26
jemten
jemten approved these changes Dec 19, 2023
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Nice work!!

@Lucpen Lucpen merged commit 042e729 into nf-core:dev Dec 19, 2023
@Lucpen Lucpen deleted the fastp branch December 19, 2023 15:28
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Add optional trimming of fastq files

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@Lucpen @jemten