save_bam_mapped + gatk_spark fails

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

https://nf-co.re/sarek

MIT License

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save_bam_mapped + gatk_spark fails #778

Open FriederikeHanssen opened 2 years ago

FriederikeHanssen commented 2 years ago

Description of the bug

Merging and saveing the mapped bams fails when using GATK spark. This is due to name-sorting the reads in this case however, for merging they need to be coordinate sorted.

We should decide if

a) no save_bam_mapped with GATK spark b) no merging and save sharded bam files c) two different sort orders ( no imho)

Command used and terminal output

No response

Relevant files

No response

System information

No response

FriederikeHanssen commented 1 year ago

We have decided that only docs should be added and maybe some input validation done in #1097