Add minimum_alignment_q_score parameter for MAPQ filtering (similar to nf-core/cutandrun)
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Description
Description of feature
In the nf-core/cutandrun pipeline, the minimum_alignment_q_score parameter (default: 20) allows explicit filtering of low-quality alignments based on MAPQ scores. However, this option is not implemented in nf-core/chipseq, despite being a common QC step for ChIP-seq data.
This was discussed in the nf-core Slack, and the team suggested opening an issue for tracking. @JoseEspinosa
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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by comparing the minimum_alignment_q_score implementation in nf-core/cutandrun with the nf-core/chipseq workflow and its parameter handling. Confirm how low-quality alignments are filtered and define completion as exposing the parameter with a default of 20 and applying it to MAPQ filtering in the ChIP-seq pipeline.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100