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fix issues with params json dump #1318

Merged
merged 2 commits into from
Nov 8, 2023
Merged

fix issues with params json dump #1318

merged 2 commits into from
Nov 8, 2023

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FriederikeHanssen
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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
  • If necessary, also make a PR on the nf-core/sarek 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 --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 Nov 7, 2023

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit f996c2f

+| ✅ 144 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: bcftools_annotations
  • schema_description - No description provided in schema for parameter: bcftools_annotations_index
  • schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-07 22:01:13

@asp8200
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asp8200 commented Nov 8, 2023

Looks good. I'll try to test it :-)

@FriederikeHanssen FriederikeHanssen merged commit 13eb2c9 into nf-core:dev Nov 8, 2023
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@asp8200
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asp8200 commented Nov 8, 2023

I can confirm that now that params_<ts>.json is placed on s3 and no longer on the hard disk. Sarek no longer creates that subfolder called s3:.... on the disk.

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@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @asp8200 @maxulysse