4 commits

Author	SHA1	Message	Date
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
FriederikeHanssen	257078bb39	Update strelka, by enabling BP if Manta candidates are present (#923) ... * add BP to strelka/somatic * merge conflicts * update strelka modules for BP * update strelka modules for BP * apply suggestions from code review	2021-10-27 17:49:54 +02:00
FriederikeHanssen	754db250a0	Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) ... * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>	2021-10-27 16:14:52 +02:00
Harshil Patel	4e9e732b76	Add strelka/somatic module (#866) ... * Add strelka/somatic module * Fill out meta.yml properly	2021-10-18 22:34:23 +01:00