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Some updates (see below) #49

Merged
merged 10 commits into from
Jun 5, 2024
Merged

Some updates (see below) #49

merged 10 commits into from
Jun 5, 2024

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JoseEspinosa
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@JoseEspinosa JoseEspinosa commented Jun 5, 2024 •
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  • Use pipelines_testdata_base_path in configs.
  • Removed unused fastqc module.
  • Add skip_multiqc param.
  • Group "skip process" params together in schema and config.
  • Update MAKE_REPORT image (nf-core registry for release)

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented Jun 5, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 27ffd9c

+| ✅ 212 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗  10 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-05 11:23:51

itrujnara
itrujnara approved these changes Jun 5, 2024
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Looks good, thanks for the tweaks

conf/test.config
@@ -20,7 +20,7 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/reportho/testdata/samplesheet/samplesheet.csv'
input = pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet.csv'
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I preached nf-core/modules#5281 and forgot about it myself, shame on me

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No worries! 😄

@JoseEspinosa JoseEspinosa merged commit 56baec0 into nf-core:dev Jun 5, 2024
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@itrujnara itrujnara itrujnara approved these changes

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@JoseEspinosa @itrujnara