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Adding the sequencing center was done a while ago to have properly set ReadGroups in the BAM files created by HiSAT2 or STAR. However, this isn't enough when using any tool or library based on the picard/GATK htsjdk, that checks for certain required readgroup information to be present in BAM files and corresponding headers (not only when sequencing center is set, but in all cases!). This caused QualiMap to fail unfortunately, which @olgabot found out here: #238
This PR adds the
SM
information to both HISAT2 and STAR and adds in the defaults without sequencing centers to be added in all cases, otherwise QualiMap will also fail when seqCenter isn't set by the user!PR checklist
nextflow run . -profile test,docker
).nf-core lint .
).docs
is updatedCHANGELOG.md
is updatedREADME.md
is updatedHappy to add more RG information, if this is necessary (we should maybe test/check this out @olgabot ?)