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Add ability to save assembly-mapped reads#494

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jfy133 merged 2 commits intonf-core:devfrom
jfy133:save-mapped-reads
Aug 16, 2023
Merged

Add ability to save assembly-mapped reads#494
jfy133 merged 2 commits intonf-core:devfrom
jfy133:save-mapped-reads

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@jfy133 jfy133 commented Aug 16, 2023

closes #487

(breaking my own rule, but very simple change while we are waiting for final CAT bugfix)

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  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
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@jfy133 jfy133 changed the base branch from master to dev August 16, 2023 15:51
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github-actions Bot commented Aug 16, 2023

This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @jfy133,

It looks like this pull-request is has been made against the jfy133/nf-core-mag master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the jfy133/nf-core-mag dev branch.

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Thanks again for your contribution!

@jfy133 jfy133 requested review from CarsonJM and d4straub August 16, 2023 15:53
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github-actions Bot commented Aug 16, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6bdbad0

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-16 15:55:09

prototaxites
prototaxites reviewed Aug 16, 2023
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Comment thread conf/modules.config
pattern: "*.log"
],
[
path: { "${params.outdir}/Assembly/${assembly_meta.assembler}/QC/${assembly_meta.id}" },
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@prototaxites prototaxites Aug 16, 2023 •
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Maybe Assembly/${assembly_meta.assembler}/(bams|maps)/${assembly_meta.id} or similar? Or even AssemblyMaps/${assembly_meta.assembler}/${assembly_meta.id}/? Not sure that bams/bais fit into the context of 'QC'!

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@CarsonJM CarsonJM Aug 16, 2023

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I think QC would be okay because the alignment can be used to quality check the assemblies, but agree that keeping it broader (like bam/maps) might work better because these BAM files have other uses as well.

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Exactly, I'm keeping them alongside where the bowtie2 log file is saved... I don't want to rock the boat too much v😬

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@jfy133 jfy133 Aug 16, 2023

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If you agree we can reconfigure the output in the future, then could you give a ✅!

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jfy133 commented Aug 16, 2023

Thanks @CarsonJM (and @prototaxites !)

@jfy133 jfy133 merged commit 2090c56 into nf-core:dev Aug 16, 2023
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@prototaxites prototaxites prototaxites left review comments

@CarsonJM CarsonJM CarsonJM approved these changes

@d4straub d4straub Awaiting requested review from d4straub d4straub is a code owner

@alexhbnr alexhbnr Awaiting requested review from alexhbnr

@maxibor maxibor Awaiting requested review from maxibor

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Add option to export BAM file with reads aligned against the contigs to results folder

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@jfy133 @prototaxites @CarsonJM