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Fixed the bug in the filtering of multiple PacBio files #78

Merged
merged 4 commits into from
May 24, 2024
Merged

Fixed the bug in the filtering of multiple PacBio files #78

merged 4 commits into from
May 24, 2024

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gq1
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@gq1 gq1 commented May 24, 2024

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).

@gq1 gq1 self-assigned this May 24, 2024
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This PR is against the main 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 @gq1,

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

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

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github-actions bot commented May 24, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit fba4492

+| ✅ 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 2024-05-24 10:27:31

@gq1 gq1 linked an issue May 24, 2024 that may be closed by this pull request
Fix when multiple PacBio files are given #77
Closed
@gq1 gq1 requested a review from muffato May 24, 2024 09:42
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gq1 commented May 24, 2024 •
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I copied all the changes from readmapping PR to here sanger-tol/readmapping#90
The testing data not being copied and the originally single copy of data run fine.

This PR being blocked because we are trying to merge to protected main branch directly. This is a bug fix so it will be OK and we will force to merge.

The readmpping pipeline CI set the protection branch as master, that is why the block check not being done.
https://github.com/sanger-tol/readmapping/blob/a27e9ce841d230f3c1ca5086019a134a116bee18/.github/workflows/branch.yml#L6

muffato
muffato reviewed May 24, 2024
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muffato
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muffato
muffato approved these changes May 24, 2024
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We're not good with typing text today :) but we got there in the end !

@gq1 gq1 merged commit 8025881 into main May 24, 2024
6 of 7 checks passed
@muffato muffato deleted the pacbio_fix branch May 24, 2024 10:50
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Fix when multiple PacBio files are given
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