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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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fix: update samtools.yaml to latest `1.17` and update github actions #75

Closed dlaehnemann closed 1 year ago

dlaehnemann commented 1 year ago

@manuelphilip Was there a reason for the old version of samtools =1.9? Otherwise I would update this to the latest version.

I found this, because we were seeing very large memory usage (> 20GB) for the rule get_mapped_canonical_transcripts, which should stream through the BAM (and the BAMs we had were below 1GB), so I wouldn't expect any large memory usage. The only explanation I have so far, is that maybe this very old version of samtools somehow had a bug or very suboptimal handling of BAM files.

manuelphilip commented 1 year ago

Hi @dlaehnemann , sure you can update it to latest version and it should run