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stjude / XenoCP

A cloud-based tool for mouse read cleansing in xenograft samples
Apache License 2.0
5 stars 3 forks source link

Rewrite BAM header #38

Open adthrasher opened 1 year ago

adthrasher commented 1 year ago

Rewrite the BAM header to remove duplicate @CO records that result from splitting and merging the BAM file. Also, add a @PG record to record the XenoCP run.

Also updates the version of STAR and BWA to match what is being used in the St. Jude Cloud workflows repository. Without this change, the CWL and WDL workflows would use different aligner versions.

adthrasher commented 1 year ago

@mcrusch - This isn't ready for a full review but wanted to at least get a preliminary opinion. I don't really like manipulating the BAM header like this, but since XenoCP is a collection of steps, there didn't seem to be a natural place to make the edits. So I opted for adding a script to the end of the pipeline.