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Qc on speed: FastP and Mosdepth as drop-in replacement for Trimgalore/Seqkit & Deeptools/qualimap#596

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FriederikeHanssen merged 38 commits intonf-core:devfrom
FriederikeHanssen:qc_on_speed
Jun 24, 2022
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Qc on speed: FastP and Mosdepth as drop-in replacement for Trimgalore/Seqkit & Deeptools/qualimap#596
FriederikeHanssen merged 38 commits intonf-core:devfrom
FriederikeHanssen:qc_on_speed

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@FriederikeHanssen FriederikeHanssen commented Jun 19, 2022 •
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Close #508

cc #95

TODO:

  • Update Fastp module to not have .trim in the output (confusing when it is just used for splitting
  • UMI subworkflow: incooporation into FastP?
  • Add test for trimming
  • Update subway map
  • Update docs
  • Make sure MultiQC has all plots
  • Document new parameters, update modules.config

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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 Jun 19, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5851733

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-24 16:07:22

FriederikeHanssen
FriederikeHanssen commented Jun 24, 2022
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Comment thread conf/modules.config Outdated
params.split_fastq > 0 ? "--split_by_lines ${params.split_fastq * 4}" : "",

// For trimgalore also auto detection was used
//params.adapter_R1 ? "--adapter_sequence ${params.adapter_R1}" : "", //normally not needed
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@FriederikeHanssen FriederikeHanssen Jun 24, 2022

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should we provide the additonal parameter for setting specific adapter sequences? Wasn't supported before, but trimgalore guessed the adapter (same here at the moment by default) @maxulysse

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review June 24, 2022 13:13
ggabernet
ggabernet reviewed Jun 24, 2022
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I had some comments, but otherwise looks good!

Comment thread conf/modules.config
Comment thread tests/test_recalibrate.yml
Comment thread workflows/sarek.nf
Comment thread workflows/sarek.nf
ggabernet
ggabernet approved these changes Jun 24, 2022
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Looks good to me!

@FriederikeHanssen FriederikeHanssen merged commit fe25216 into nf-core:dev Jun 24, 2022
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@ggabernet ggabernet ggabernet approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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