CSI bam index not working
A pull request for this has already been merged.
- #328 by @bjlang — merged
- Dominant language
- Nextflow
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Description
Description of the bug
With large genomes, the .bai index file format is insufficient so .csi file format is specified by "ext.args='-c'" in SAMTOOLS_INDEX.
The pipeline first fails with a docker timeout error. Upon -resume it completes "without errors" but skips most processes.
FASTQ_ALIGN_BWA can output .csi file but lines 165-177 of atacseq.nf seems to only allow .bai in ch_genome_bam_index.
Command used and terminal output
No response
Relevant files
System information
No response
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Inspect atacseq.nf lines 165-177, where ch_genome_bam_index is described as allowing .bai files, and compare that with the .csi output from FASTQ_ALIGN_BWA when SAMTOOLS_INDEX uses '-c'. Check the pipeline's resume behavior with a large-genome CSI index; done means the index is accepted and downstream processes are not skipped.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100