Auto-Save Index Files Alongside BAMs #446
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Some small optimizations too.
…ally too large to benefit from Steve's ComputeAllowedLocalSSD optimization.
…and conversion to .g.vcf.bgz steps
- Local disk to SSD
- samtools index -@ 2 ~{basename(prefix)}
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Overview:
This branch is built on top of jts_kvg_sp_malaria branch. This PR improves our BAM file indexing process by ensuring index files are automatically saved alongside BAM files.
Key Updates:
outdirparameter inSRIndexBamworkflow is now optional. The workflow places.baifiles next to their.bamfiles ifoutdirisn't provided.Adjusted
FinalizeBamIndexto automatically detect and use the BAM file directory for storing.baifiles.Benefits:
Ensures .bai files are easily accessible for analysis.
Testing:
Tests confirm correct
.baifile placement in specified and derivedoutdircases, ensuring reliability across various scenarios.