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update modules #671

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update modules #671

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maxulysse
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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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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4b72d71

+| ✅ 146 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_description - No description provided in schema for parameter: ascat_ploidy

❔ 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 2022-07-20 13:20:55

SusiJo
SusiJo approved these changes Jul 20, 2022
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LGTM! Let's hope all checks pass 🤞

FriederikeHanssen
FriederikeHanssen reviewed Jul 20, 2022
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modules/nf-core/modules/samtools/merge/main.nf
@@ -8,8 +8,9 @@ process SAMTOOLS_MERGE {
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"

input:
tuple val(meta), path(input_files)
tuple val(meta), path(input_files, stageAs: "?/*")
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I am a bit worried about this stageAs thing

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it's in the intput, I'm less worried about that

maxulysse
maxulysse commented Jul 20, 2022
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modules/nf-core/modules/samtools/merge/main.nf
path fasta
path fai
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I wasn't sure about adding the fai in the path for the cram files

@maxulysse maxulysse changed the title update modules, hopefully for the last time before the release update modules Jul 20, 2022
@maxulysse maxulysse added this to the 3.1 milestone Jul 20, 2022
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DO NOT MERGE BEFORE RELEASE

FriederikeHanssen
FriederikeHanssen requested changes Jul 20, 2022
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merge after release

@maxulysse maxulysse closed this Jul 25, 2022
@SusiJo SusiJo mentioned this pull request Jul 26, 2022
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@maxulysse maxulysse deleted the dev_update_modules branch September 5, 2022 12:25
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen requested changes

@SusiJo SusiJo SusiJo approved these changes

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@maxulysse @FriederikeHanssen @SusiJo