Add fq2bam to methylseq

[eduard-watchmaker]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
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[eduard-watchmaker]

we don't need this in all the runs, just on the tests

[eduard-watchmaker]

we don't need this since we publish the *markdup.sorted.bam and .bai

[eduard-watchmaker]

@nf-core-bot fix linting

[eduard-watchmaker]

@nf-core-bot fix linting

[eduard-watchmaker]

The linting really is giving me a hard time lol

[eduard-watchmaker]

Tests 2 for conda, singularity and docker show different snapshots for the 'latest' version vs the 25.04, unsure why.

[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: 3.5.1.
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.

[FelixKrueger]

Thanks a lot for this, @eduard-watchmaker! 🙏

Since this PR was opened, parabricks/fq2bam has already landed on dev: the module is installed under modules/nf-core/parabricks/fq2bam/ and wired into the fastq_align_dedup_bwamem subworkflow with the same design this PR uses — a use_gpu gate, output_fmt, known_sites, and ch_alignment = PARABRICKS_FQ2BAM.out.bam. It came in via #610 (Update Bismark to 3.0.0 and modernise alignment modules/subworkflows), at a newer module pin (f0b0dc3… vs this PR's 1e4345f…).

That makes this PR superseded — its core purpose (adding fq2bam to the bwa-mem path) is already on dev, and it's ~37 commits behind with conflicts on the fq2bam module files themselves. So I'm closing it to keep the queue tidy.

The only thing here not on dev is a small conf/modules/parabricks_fq2bam.config; dev's fq2bam runs fine without it, but we can add process-level config as a quick standalone follow-up if it turns out to be useful.

Really appreciate the contribution — the approach matched exactly where dev landed. 🙌