Adding targeted analysis to nf-core/methylseq pipeline

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This project focuses on developing a targeted analysis for methylseq data in the nf-ccore/methylseq pipeline. We’re planning to add the following features:

• --targeted parameter: Currently, all detected methylation signals are included in the final results. However, some enrichment protocols target specific genomic regions. To address this, we propose adding a --targeted parameter that allows filtering results to retain only on-target methylation signals. The input would be a BED file specifying the target regions.
• Enrichment metrics: Building on this idea, we propose adding a job to calculate on-target vs. off-target fractions of aligned reads, along with other enrichment metrics. A tool like CollectHsMetrics from Picard could be used for this purpose. There’s already an open PR related to this, which we’d be happy to contribute to.

Goals

• Enrichment filtering results.
  • For people interested in Nextflow module development and targeted methylation sequencing analysis.
• Ensuring smooth integration with existing pipeline components.
  • For contributors with experience in nf-core module structure and dependencies.
• Create enrichment metrics using Picard CollectHsMetrics.
  • For users that would like to integrate an existing nf-core module into a new pipeline.

We welcome contributors of all experience levels.