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Rework of the output directories #8

Merged
merged 2 commits into from
Oct 10, 2023
Merged

Rework of the output directories #8

merged 2 commits into from
Oct 10, 2023

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muffato
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@muffato muffato commented Aug 4, 2023

As per https://jira.sanger.ac.uk/browse/TOLIT-1559 we want the output directories to be "analysis" directories rather than "species" directories.

I'm using the convention that I'm already using in the sequencecomposition pipeline: each assembly has got its own outdir in its meta. So essentially, the output directories are defined as meta.outdir which either comes from the outdir column of the sample-sheet, or from the --outdir command-line parameter for one-off downloads.

I have also removed the mechanism to automatically find the accession number from the ACCESSION file when the output directory matches the ToL structure. The accession number will be available and it's better to be explicit.

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
  • 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).

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github-actions bot commented Aug 4, 2023 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 27b5e8a

+| ✅ 131 tests passed       |+
#| ❔  22 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: assets/multiqc_config.yml
  • files_exist - File is ignored: assets/nf-core-ensemblgenedownload_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: docs/images/nf-core-ensemblgenedownload_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-ensemblgenedownload_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-ensemblgenedownload_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-ensemblgenedownload_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-ensemblgenedownload_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/ensemblgenedownload/ensemblgenedownload/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-09-23 11:16:16

Base automatically changed from template_update to dev August 11, 2023 09:45
@muffato muffato marked this pull request as ready for review August 11, 2023 17:04
priyanka-surana
priyanka-surana approved these changes Oct 3, 2023
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LGTM 👍🏼 Thanks!

@muffato muffato merged commit 04b7a5e into dev Oct 10, 2023
@muffato muffato deleted the outdir branch October 10, 2023 09:12
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@priyanka-surana priyanka-surana priyanka-surana approved these changes

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