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Re-add piping, and hope ARFP2 doesn't pipe errors into files anymore … #845

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jfy133 merged 2 commits into from
Mar 17, 2022
Merged

Re-add piping, and hope ARFP2 doesn't pipe errors into files anymore … #845

jfy133 merged 2 commits into from
Mar 17, 2022

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@jfy133 jfy133 commented Mar 10, 2022

…(only reported at one cluster)
for the one and online ashildv

Fixes #843

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
    • If necessary, also make a PR on the nf-core/eager 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).
  • 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).

@jfy133 jfy133 added the WIP Work in progress label Mar 10, 2022
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github-actions bot commented Mar 10, 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!

@jfy133 jfy133 requested a review from a team March 10, 2022 14:23
TCLamnidis
TCLamnidis approved these changes Mar 17, 2022
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LGTM.
Glad to hear ashildv is "one and online".

@jfy133 jfy133 merged commit 9a66d39 into dev Mar 17, 2022
@jfy133 jfy133 deleted the arfp-pigz-fix branch March 17, 2022 15:55
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github-actions bot commented Mar 17, 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 mentioned this pull request Mar 24, 2022
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