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Samtools view #85

Merged
merged 1 commit into from
Jun 25, 2024
Merged

Samtools view #85

merged 1 commit into from
Jun 25, 2024

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muffato
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@muffato muffato commented Jun 24, 2024 •
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TOLIT-1817: Use the upstream version of samtools_view, which now supports the unoutput (now called unselected) output channel.

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 - have you followed the pipeline conventions in the contribution docs
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@muffato muffato added the maintain Tasks to keep pipelines up to date label Jun 24, 2024
@muffato muffato requested a review from gq1 June 24, 2024 16:47
@muffato muffato self-assigned this Jun 24, 2024
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github-actions bot commented Jun 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d879a5f

+| ✅ 125 tests passed       |+
#| ❔  26 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: CODE_OF_CONDUCT.md
  • files_exist - File is ignored: assets/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-variantcalling_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-variantcalling_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/variantcalling/variantcalling/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-06-24 16:48:59

@muffato muffato requested review from tkchafin and removed request for gq1 June 24, 2024 19:27
@muffato muffato changed the base branch from dev to align_flag June 25, 2024 08:48
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gq1 commented Jun 25, 2024

Samtools version also being up0dated from 1.17 to 1.20

Base automatically changed from align_flag to dev June 25, 2024 09:32
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muffato commented Jun 25, 2024

Samtools version also being up0dated from 1.17 to 1.20

Yep. Something to add to the CHANGELOG when we prepare the release

@muffato muffato merged commit 45b571a into dev Jun 25, 2024
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@muffato muffato deleted the samtools_view branch June 25, 2024 12:21
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@tkchafin tkchafin tkchafin approved these changes

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