Fixed the bug in the filtering of multiple PacBio files

gq1 commented 1 month ago

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).

github-actions[bot] commented 1 month ago

This PR is against the `main` branch :x:

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!

github-actions[bot] commented 1 month ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit fba4492

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

### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.1.3'`` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-variantcalling_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-variantcalling_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-variantcalling_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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gq1 commented 1 month ago

I copied all the changes from readmapping PR to here https://github.com/sanger-tol/readmapping/pull/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

sanger-tol / variantcalling