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Pileupcaller paths fix #909

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Merged
jfy133 merged 3 commits into from
Jul 29, 2022
Merged

Pileupcaller paths fix #909

jfy133 merged 3 commits into from
Jul 29, 2022

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@TCLamnidis
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@TCLamnidis TCLamnidis commented Jul 28, 2022

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

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

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github-actions bot commented Jul 28, 2022

Markdown 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 markdownlint-cli
  • Fix the markdown errors
    • Automatically: markdownlint . --config .github/markdownlint.yml --fix
    • Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@TCLamnidis TCLamnidis requested a review from jfy133 July 28, 2022 16:37
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github-actions bot commented Jul 28, 2022

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
  • 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 👍

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

@jfy133 jfy133 merged commit 93301b7 into endorspy-resume-fix Jul 29, 2022
@jfy133 jfy133 deleted the pileupcaller_paths_fix branch July 29, 2022 06:33
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@jfy133 jfy133 jfy133 approved these changes

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3 participants

@TCLamnidis @jfy133