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Set publish mode for FastQs #155

Merged
merged 2 commits into from
Dec 12, 2023
Merged

Set publish mode for FastQs #155

merged 2 commits into from
Dec 12, 2023

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edmundmiller
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@edmundmiller edmundmiller commented Nov 23, 2023 •
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I think this was set to avoid duplicate copying of the raw fastqs, and assuming most people would run them through fastp.

I'm not opposed to changing this to only publish if --skip_tools "falco,fastp" is set or a param like publish_fastq is opted in to.

Closes #154

@edmundmiller edmundmiller self-assigned this Nov 23, 2023
@edmundmiller edmundmiller changed the base branch from master to dev November 23, 2023 15:18
@edmundmiller edmundmiller requested a review from a team as a code owner November 23, 2023 15:18
@nf-core nf-core deleted a comment from github-actions bot Nov 23, 2023
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github-actions bot commented Nov 23, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5e47d29

+| ✅ 156 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • 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 WorkflowDemultiplex.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-12-12 20:46:48

@edmundmiller edmundmiller linked an issue Nov 23, 2023 that may be closed by this pull request
No fastq.gz in NA folder after usage of --skip_tools "falco,fastp" #154
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@edmundmiller edmundmiller added this to the 1.4.0 milestone Nov 23, 2023
@edmundmiller edmundmiller requested review from maxulysse and Aratz and removed request for matthdsm December 11, 2023 18:35
Aratz
Aratz approved these changes Dec 12, 2023
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Looks good to me 👍

I think this is good enough for a default config. If users want to avoid copying theses files to save space, they can either set the publish mode to another value or write their own custom config.

Also, looks like the tests are failing because GHA is trying to run them with an old version of nextflow:

We don't need to test with nextflow 22.10 anymore do we?

@edmundmiller edmundmiller mentioned this pull request Dec 12, 2023
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Great catch! Let's see if that fixes it! 🙃

@edmundmiller edmundmiller merged commit 290c07b into dev Dec 12, 2023
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@edmundmiller edmundmiller deleted the mode branch December 12, 2023 21:03
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@Aratz Aratz Aratz approved these changes

@maxulysse maxulysse Awaiting requested review from maxulysse

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No fastq.gz in NA folder after usage of --skip_tools "falco,fastp"
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