Targeted analysis

[dcarrillox]

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>).
  • singularity instead of docker
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  • singularity instead of docker
• 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).

Targeted analysis

As outlined in #511, we have introduced additional steps to enhance the analysis of targeted methylation protocols such as the TWIST human methylome panel:

1. Filtering bedGraph files, to contain only positions listed in a provided BED with target regions.
2. Running CollectHsMetrics from Picard, to assess the performance of the enrichment. There was Hs metrics #313 already open for this matter.

New Subworkflow and Parameters

To support these updates, we created a new local subworkflow called targeted_sequencing. The following parameters control the targeted analysis:

• --run_targeted_sequencing (boolean). Instructs the pipeline to perform the targeted analysis, which by default only filters the bedGraph files.
• --target_regions_file (file path). BED file containing the target regions
• --run_picard_collecthsmetrics (boolean). Run also CollectHsMetrics using the provided BED file and sample BAM files.

Additional changes

We have also modified some parameters and introduced new ones:

• --comprehensive parameter:

  • Currently this parameter is available in both bismark and bwameth_methyldackel workflows but behaves differently:
    • In bismark, it merges methylation results regardless of strand (documentation).
    • In bwameth_methyldackel, this parameter does not exist in standalone MethylDackel. In the pipeline's implementation, it enables methylation calling at CHG and CHH contexts.
  • Change: We removed this parameter from the bwameth_methyldackel workflow. In the bismark workflow, we have decoupled --merge_non_CpG from --comprehensive (CG CHG and CHH with --comprehensive flag using bismark workflow #388).

• New parameters for bwameth workflow:

  • --all_contexts: Enables methylation calling at CHG and CHH contexts.
  • --merge_context: Runs MethylDackel with --mergeContext. This addresses Addition of --mergeContext for MethylDackel #460.