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Add bam output for Preprocessing#594

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FriederikeHanssen merged 15 commits intonf-core:devfrom
FriederikeHanssen:output_bam
Jun 21, 2022
Merged

Add bam output for Preprocessing#594
FriederikeHanssen merged 15 commits intonf-core:devfrom
FriederikeHanssen:output_bam

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@FriederikeHanssen FriederikeHanssen commented Jun 17, 2022

Closes #437

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).

@FriederikeHanssen FriederikeHanssen changed the title Add bam output for recalibration Add bam output for Preprocessing Jun 17, 2022
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github-actions Bot commented Jun 17, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7cf0f7c

+| ✅ 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 2022-06-21 13:49:54

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FriederikeHanssen commented Jun 17, 2022

@maxulysse it works, it could be more efficient around the MD part. MD -> BAMTOCRAM -> QC (-> CRAMTOBAM). Unsure how much effort we should put in here.

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review June 20, 2022 20:03
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FriederikeHanssen commented Jun 20, 2022

Not sure why I didn't think about this before, but now just publishing out of markduplicates in case --save_output_as_bam is set. For spark still a conversion done, but it shouldn't matter if MD_SPARK outputs cram that we convert to bam for this parameter or if it produces BAM that we then need to convert to CRAM for the remaining pipeline

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FriederikeHanssen commented Jun 21, 2022

@nf-core-bot please fix prettier

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FriederikeHanssen commented Jun 21, 2022

@nf-core-bot please fix linting

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FriederikeHanssen commented Jun 21, 2022 •
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🤨 ran prettier locally and CHANGELOG is fine/ nothing to commit. @maxulysse how do I make the bot help me?

prettier --check CHANGELOG.md
Checking formatting...
All matched files use Prettier code style!

maxulysse
maxulysse approved these changes Jun 21, 2022
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<3
I love how you get the extension for the csv file

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maxulysse commented Jun 21, 2022

@nf-core-bot fix linting pretty please

@FriederikeHanssen FriederikeHanssen merged commit 67c2546 into nf-core:dev Jun 21, 2022
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