nf-core_modules/modules/manta
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
..
germline Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
somatic Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
tumoronly Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00