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Remove local + update modules + nf-corize mapping subworkflow #466

Merged
merged 5 commits into from
Dec 9, 2021
Merged

Remove local + update modules + nf-corize mapping subworkflow #466

merged 5 commits into from
Dec 9, 2021

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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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github-actions bot commented Dec 8, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 113e37b

+| ✅ 135 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 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 test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • 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
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.2.dev0
  • Run at 2021-12-08 22:44:53

@maxulysse
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leftovers from #462
I'd like to merge after #464

@FriederikeHanssen FriederikeHanssen self-requested a review December 9, 2021 08:00
FriederikeHanssen
FriederikeHanssen reviewed Dec 9, 2021
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modules/nf-core/modules/bwamem2/mem/main.nf
def prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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should this go to the modules.config as well? seem to be the same to me as the status line basically

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The read_group you mean?

@maxulysse maxulysse merged commit 085f1df into nf-core:dev Dec 9, 2021
@maxulysse maxulysse deleted the dev_mapping branch December 9, 2021 08:57
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen