implement the bam_csi_index parameter in atacseq pipeline
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Description
Description of feature
I had success when running atacseq (-r 2.1.2) for samples with small genome. When I tried to run other samples with big genome and one of the chromosome size is larger than 500Mb. I set the "--bam_csi_index". However, I still got error message "....cannot be stored in a bai index. Try using a csi index". It seems the atacseq pipeline does not implement the bam_csi_index parameter. It would be greatly appreciated if this parameter can be implemented in atacseq pipeline.
Contributor guide
First steps
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Research direction
Start by locating the atacseq pipeline's parameter declaration and BAM indexing step. Check how the existing bam_bai_index behavior is wired and how --bam_csi_index is passed through. Done means large genomes can use a CSI index without the BAI size error; add or update coverage for that parameter if the repository has relevant tests.
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