flexibility of bam header for different platforms

[kew24]

Currently, ILLUMINA is hardcoded in as the platform in the bam header. With more platforms being used in the genomics core (particularly ELEMENT and ONT), we should provide flexibility in config.yaml for users to specify this for proper labeling.

variants-gatk4/Snakefile

Line 197 in 673196e

bwa_RG='"@RG\\tID:{sample}\\tLB:{sample}\\tPL:ILLUMINA\\tSM:{sample}"',

See more info on accepted PL values in the sam/bam hts specs.

I can get to this when I have time – currently I'm just changing the hardcoded value in my clone of the repo for certain projects where applicable.

[genomics-kl]

That's a good point. Thanks for bringing this up.