Skip fastqc

[jorondo1]

PR checklist

Please keep in mind this is my first ever "real" pull request, i-e in a collaborative setting. I'm hoping I did everything right!

Changes:

Added --skip_fastqc switch (default: false) that skips both FASTQC_RAW and FASTQC_TRIMMED steps in short-read preprocessing. Lot of it is redundant with fastp reports, which is sufficient for me. Parameter is declared in nextflow_schema.json and handled conditionally in subworkflows/local/shortread_preprocessing.nf

• If you've fixed a bug or added code that should be tested, add tests!

Code lint

This is new to me, I feel like the warnings and errors here do not concern what I’ve modified but I’m not sure if there’s something I should be doing about them?

╭─ [?] 1 Pipeline Test Ignored ────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_unchanged: File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 2 Pipeline Test Warnings ───────────────────────────────────────────────────────────────────────────────╮
│ │
│ nextflow_config: Config manifest.version should end in dev: 5.4.2 │
│ nfcore_yml: nf-core version in .nf-core.yml is not set to the latest version. Should be 3.4.1 but was 3.5.2 │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 2 Pipeline Tests Failed ────────────────────────────────────────────────────────────────────────────────╮
│ │
│ files_unchanged: .github/workflows/linting.yml does not match the template │
│ files_unchanged: assets/nf-core-mag_logo_light.png does not match the template │
│ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

– [x] Tests

-[nf-core/mag] Pipeline completed successfully, but with errored process(es) -
Completed at: 23-Jun-2026 13:47:58
Duration    : 30m 55s
CPU hours   : 1.8 (0,4% failed)
Succeeded   : 195
Ignored     : 1
Failed      : 1

with
`[de/1c4d8d] NFCORE_MAG:MAG:BINNING:MAXBIN2 (test_minigut_sample2) | 4 of 4, ignored: 1 ✔

– [x] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
not sure what to look for here, I do see

WARN: Access to undefined parameter `skip_tiara` -- Initialise it to a default value eg. `params.skip_tiara = some_value`

• Usage Documentation in docs/usage.md is updated.
  N/A

• Output Documentation in docs/output.md is updated.
  N/A

• CHANGELOG.md is updated.
  Wasn’t sure how to do this since it’s not a release, so I left a note. Again this is all pretty new to me!

• README.md is updated (including new tool citations and authors/contributors).
  N/A

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.2.
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.