Taps

[eduard-watchmaker]

Added TAPS to methylseq

This pull request aim to add support for TAPS data in the nf-core/methylseq pipeline.

We added the subworkflow FASTQ_ALIGN_DEDUP_BWAMEM (bwa mem) to align TAPS data (positive readout / conversion of methylated Cs instead of all unmethylated Cs).

We separated MethylDackel from the alignment subworkflow fastq_align_dedup_bwameth.

We created a new subworkflow called BAM_METHYLDACKEL with the two different methyldackel processes available.

We added a subworkflow to evaluate methylation of bwa mem or bwa-meth aligned reads called 'BAM_TAPS_CONVERSION' which used different rastair tools.

We added the logic to have data flow from either aligner into either methylation caller.

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
• If necessary, also make a PR on the nf-core/methylseq branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[sateeshperi]

not sure we want to turn this on by default in the pipeline....there could be large files that will quickly cause disk space issues. Users can provide this via their custom config as needed

[eduard-watchmaker]

This was updated on the original parabricks modules in nf-core, I just updated them to the latest version. I suggest we bring this conversation there if we have concerns.

[eduard-watchmaker]

No idea why the linting fails, it works perfectly on my computer using nf-core/tools version 3.5.0.dev0

[eduard-watchmaker]

Overall changes in TAPS methylseq PR: #574:

Updated bismark modules

Added rastair modules: nf-core/modules#9065

Removed methyldackel modules from fastq_align_dedup_bwameth subworkflow: nf-core/modules#9068

Added bam_methyldackel subworkflow which runs methyldackel modules: nf-core/modules#9066

Added fasta_index_methylseq subworkflow which indexes genomes for bismark, bwa-meth or bwa mem: nf-core/modules#9067

Added bam_taps_conversion to run rastair modules for TAPS data: nf-core/modules#9104

Added fastq_align_dedup_bwamem subworkflow to run bwa mem (+ gpu parabricks), dedup and run stats: nf-core/modules#9197

Refactored the main METHYLSEQ workflow to add the logic for TAPS, also added changes to metromap and docs

Each of these PRs came with auxiliary modules and conf files when needed, as well as all their tests, meta.yml files and snapshots.