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Add 'auto' option to fastq_dir_to_samplesheet.py and set as default argument #956

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merged 3 commits into from
Mar 14, 2023
Merged

Add 'auto' option to fastq_dir_to_samplesheet.py and set as default argument #956

merged 3 commits into from
Mar 14, 2023

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ryanyord
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Updated the fastq_dir_to_samplesheet.py to add the 'auto' option to concur with #729. Also, set this to be the default argument when generating the spreadsheet.

@drpatelh
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Awesome! Thanks @ryanyord ! Be great if you can add a line in the CHANGELOG regarding these changes. I have sent you an invite to join the nf-core Github org too.

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github-actions bot commented Mar 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 78d4dc9

+| ✅ 153 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: '3.10.1'
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-03-14 19:14:17

@drpatelh
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Python Black frustrations!! I'll merge and fix in a follow up PR.

@drpatelh drpatelh merged commit 7e187c6 into nf-core:dev Mar 14, 2023
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Python linting (black) 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 black: pip install black
  • Fix formatting errors in your pipeline: black .

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

We highly recommend setting up Black 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!

@ryanyord ryanyord deleted the samplesheet branch March 14, 2023 21:34
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2 participants
@ryanyord @drpatelh