bam_csi_index parameter for ATACSeq
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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.
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First steps
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Research direction
Start at the atacseq pipeline entry point and search for the existing bam index parameter and the step that creates or expects a BAI index. Trace how parameters are passed through the workflow, then verify that setting bam_csi_index selects CSI indexing for genomes with chromosomes larger than 500 Mb.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100