FriederikeHanssen ac1e6df076 Update to allow cram + update needed to use the gatk4 modules in sarek (#976) ... * Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>		2021-10-29 13:01:05 +02:00
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main.nf	Update to allow cram + update needed to use the gatk4 modules in sarek (#976)	2021-10-29 13:01:05 +02:00
test.yml	Update to allow cram + update needed to use the gatk4 modules in sarek (#976)	2021-10-29 13:01:05 +02:00