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Rework of the output directories #12

Merged
merged 2 commits into from
Oct 4, 2023
Merged

Rework of the output directories #12

merged 2 commits into from
Oct 4, 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.

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 403f469

+| ✅ 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-insdcdownload_logo_light.png
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: docs/images/nf-core-insdcdownload_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-insdcdownload_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-insdcdownload_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-insdcdownload_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-insdcdownload_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/insdcdownload/insdcdownload/.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 11:20:04

Base automatically changed from template_update to dev August 11, 2023 09:43
@muffato muffato marked this pull request as ready for review August 11, 2023 16:55
@muffato muffato linked an issue Sep 21, 2023 that may be closed by this pull request
Pull additional metadata as header file #9
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@muffato muffato removed a link to an issue Sep 21, 2023
Pull additional metadata as header file #9
Closed
priyanka-surana
priyanka-surana approved these changes Oct 3, 2023
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LGTM 👍🏼 Thanks!

CHANGELOG.md
@@ -3,10 +3,12 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.2.0 - [date]
## v2.0.0 - [date]
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For v2 are you planning to update to the new CHANGELOG format? I personally find that more informative.

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Discussed on Slack. The answer is yes

@muffato muffato merged commit 5649f47 into dev Oct 4, 2023
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@muffato muffato deleted the outdir branch October 4, 2023 16:02
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@muffato @priyanka-surana