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FIX: nf-prov usage #1301

Merged
merged 3 commits into from
Oct 31, 2023
Merged

FIX: nf-prov usage #1301

merged 3 commits into from
Oct 31, 2023

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maxulysse
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github-actions bot commented Oct 30, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 852712c

+| ✅ 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 2023-10-30 12:12:12

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asp8200 commented Oct 30, 2023

What does exactly does this PR fix? I can run Sarek with the latest version of nf-plov, but it does give this warning:

WARN: Config setting `prov.formats` is not defined, no provenance reports will be produced

@maxulysse
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It removes the warning and produce a file

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asp8200 commented Oct 30, 2023

It removes the warning and produce a file

Ok, what is pipeline_info/manifest_${trace_timestamp}.bco.json? Should it perhaps be mentioned in output.md along with the other pipeline_info-files?

### Pipeline information

<details markdown="1">
<summary>Output files</summary>

- `pipeline_info/`
  - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
  - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and

By the way, those file names are not entirely correct. It should be execution_report_<timestamp>.html, etc.

asp8200
asp8200 approved these changes Oct 30, 2023
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LGTM

FriederikeHanssen
FriederikeHanssen approved these changes Oct 30, 2023
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thanks for fixing 🚀

@maxulysse maxulysse merged commit 820240d into nf-core:dev Oct 31, 2023
23 checks passed
@maxulysse maxulysse deleted the nfprov branch February 19, 2024 14:42
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@asp8200 asp8200 asp8200 approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @asp8200 @FriederikeHanssen