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Move fastp arguments to modules.config #75

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Move fastp arguments to modules.config #75

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SPPearce
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@SPPearce SPPearce commented Aug 2, 2024

Move the fastp arguments that turn off the adapter/read trimming into the modules.config instead of hardcoded into the module itself.

@SPPearce SPPearce requested a review from scwatts August 2, 2024 09:43
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github-actions bot commented Aug 2, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit be61d28

+| ✅ 178 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  13 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • nextflow_config - Config manifest.version should end in dev: 1.0.0
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • schema_params - Schema param panel not found from nextflow config
  • schema_params - Schema param genome_version not found from nextflow config
  • schema_params - Schema param genome_type not found from nextflow config
  • schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
  • schema_params - Schema param ref_data_panel_data_path not found from nextflow config
  • schema_params - Schema param ref_data_virusbreakenddb_path not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-08-02 09:44:13

@scwatts
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scwatts commented Aug 5, 2024

This change makes sense within the nf-core framework wrt use of process selectors to define arguments. I have to admit I'm not much of an advocate for the heavy use of process selectors to set arguments since imo it can cause some degree of obfuscation of process configuration, though this modification seems fairly straightforward.

Could you note your use-case and justification below for this change that we discussed earlier for anyone following along?

@SPPearce SPPearce marked this pull request as draft August 5, 2024 10:53
@scwatts scwatts added the enhancement New feature or request label Aug 7, 2024
@scwatts scwatts added this to the Release 2.0.0 milestone Dec 3, 2024
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@scwatts scwatts Awaiting requested review from scwatts

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