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Ensure pseudoaligner is set if pseudoalignment is not skipped #1124

Merged
merged 13 commits into from
Nov 21, 2023
Merged

Ensure pseudoaligner is set if pseudoalignment is not skipped #1124

merged 13 commits into from
Nov 21, 2023

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pinin4fjords
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We have reports of errors like:

java.lang.IllegalArgumentException: A process input channel evaluates to null -- Invalid declaration `val quant_type`

This is because we haven't ensured that the pseudoaligner is defined when pseudoalignment is not skipped. The solution:

  • Set a default pseudoalignner
  • Add an error if pseudoaligner not defined when pseudoalignment is not skipped.

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
  • If necessary, also make a PR on the nf-core/rnaseq 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 --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).

@pinin4fjords pinin4fjords changed the base branch from master to dev November 20, 2023 14:45
@github-actions GitHub Actions
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This PR is against the master 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 @pinin4fjords,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq 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 Nov 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cfd9270

+| ✅ 144 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.13.2
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in WorkflowRnaseq.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - multiqc_config

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-21 10:19:26

maxulysse
maxulysse reviewed Nov 20, 2023
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@pinin4fjords
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@nf-core-bot fix linting

drpatelh
drpatelh reviewed Nov 21, 2023
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drpatelh
drpatelh approved these changes Nov 21, 2023
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@drpatelh drpatelh left a comment

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Good to go!

@pinin4fjords pinin4fjords merged commit b7480f7 into dev Nov 21, 2023
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@pinin4fjords pinin4fjords deleted the ensure_notnull_pseudo branch November 21, 2023 10:39
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@drpatelh drpatelh drpatelh approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@pinin4fjords @maxulysse @drpatelh @nf-core-bot