Added TAPS to methylseq

[eduard-watchmaker]

Added TAPS to methylseq

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

This pull request depends (or, will not lint properly until merged) on nf-core/modules#8963

1. We added bwa mem to align TAPS data (positive readout / conversion of methylated Cs instead of all unmethylated Cs).
2. We separated MethylDackel from the alignment subworkflow fastq_align_dedup_bwameth (we issued the PR for this in nf-core/modules here: Split fastq_align_dedup_bwameth from methyldackel modules#8963). This modifies the original subworkflow and creates a new one called methyldackel with the two different methyldackel processes available.
3. We added a subworkflow to evaluate methylation of bwa mem or bwa-meth aligned reads called 'TAPS_conversion' which used different rastair tools.
4. We added the logic to have data flow from either aligner into either methylation caller.

While we wait for the rastair image to be published in biocontainers (the PR is issued and the image is working for both Docker and Singularity / apptainer; BioContainers/containers#604) the TAPS_conversion subworkflow will only be available on dockerhub using --profile docker. The image will soon be available on quay.io/biocontainers.

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).

[github-actions]

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Hi @eduard-watchmaker,

It looks like this pull-request is has been made against the watchmaker-genomics/methylseq_fresh master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the watchmaker-genomics/methylseq_fresh dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

[eduard-watchmaker]

subway diagram of the new subworkflows

[eduard-watchmaker]

TODO

[eduard-watchmaker]

TODO

[eduard-watchmaker]

TODO