Pileupcaller paths fix - Githubissues

nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline

https://nf-co.re/eager

MIT License

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Pileupcaller paths fix #909

Closed TCLamnidis closed 2 years ago

TCLamnidis commented 2 years ago

This PR corrects the staging of input bam files for the genotyping_pileupcaller process. Avoids rare cases where binding of volumes failed within singularity and caused the process to fail.

The issue was revealed when upstream changes were made to fix endorspy caching errors.

PR checklist

[x] This comment contains a description of changes (with reason).
[x] Make sure your code lints (nf-core lint .).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker).
[x] CHANGELOG.md is updated.

github-actions[bot] commented 2 years ago

Markdown linting is failing

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github-actions[bot] commented 2 years ago

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

Install yaml-lint
- Install npm then install yaml-lint (npm install -g yaml-lint)
Fix the markdown errors
- Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
- Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment :+1:

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Thanks again for your contribution!