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Move fastp arguments to modules.config

Open SPPearce opened this issue 1 year ago • 2 comments

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

SPPearce avatar Aug 02 '24 09:08 SPPearce

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 800a7a6

+| ✅ 198 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  18 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 fastp_umi_location not found from nextflow config
  • schema_params - Schema param fastp_umi_length not found from nextflow config
  • schema_params - Schema param fastp_umi_skip not found from nextflow config
  • schema_params - Schema param redux_umi_duplex_delim 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_genome_gtf not found from nextflow config
  • schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

:grey_question: Tests ignored:

:white_check_mark: Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-03-06 22:24:02

github-actions[bot] avatar Aug 02 '24 09:08 github-actions[bot]

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?

scwatts avatar Aug 05 '24 02:08 scwatts

[!WARNING] Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2. Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

nf-core-bot avatar Mar 06 '25 03:03 nf-core-bot

Further rationale for this change: https://github.com/nf-core/oncoanalyser/commit/ba241d1daae37018d4270cac28693f1445448a7f#commitcomment-149188254

scwatts avatar Mar 06 '25 03:03 scwatts

Presumably needs an entry in the CHANGELOG. What is the rational behind not trimming at all? Is the assumption that it has already been done? We could make a new global parameter that performs basic trimming From what I recall, in my case the input DNA was quite fragmented, so many of the reads had a lot of adapter contamination, which bloats all the downstream file sizes.

SPPearce avatar Mar 06 '25 08:03 SPPearce

Good catch, I'll make that change and then merge! That's right we don't perform trimming as it's assumed to have already been done. I'd like to leave the ability for users to flexibly control trimming via NF config as proposed rather than implementing a global parameter but thank you for the suggestion

scwatts avatar Mar 06 '25 09:03 scwatts