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Auto-Save Index Files Alongside BAMs #446

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@shadizaheri shadizaheri commented Apr 11, 2024

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:

  • outdir parameter in SRIndexBam workflow is now optional. The workflow places .bai files next to their .bam files if outdir isn't provided.

  • Adjusted FinalizeBamIndex to automatically detect and use the BAM file directory for storing .bai files.

Benefits:
Ensures .bai files are easily accessible for analysis.

Testing:
Tests confirm correct .bai file placement in specified and derived outdir cases, ensuring reliability across various scenarios.

jonn-smith and others added 30 commits January 10, 2023 12:33
…ally too large to benefit from Steve's ComputeAllowedLocalSSD optimization.
jonn-smith and others added 27 commits December 4, 2023 16:22
@shadizaheri shadizaheri marked this pull request as ready for review April 11, 2024 19:46
- Local disk to SSD

- samtools index -@ 2 ~{basename(prefix)}
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4 participants