* new mitochondria mode added, tests updated to allow for temp fix for test data
* add cram test
* bam/bam_idx renamed to input and input_index
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
* added output channel for stats file, updated meta yml with description and test yml with check for stats file
* Update modules/gatk4/mutect2/main.nf
Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* mutect2 files added, first draft of module code entered
* removing comment from main.nf
* removing comment from main.nf
* test added, commit made before editing yaml
* tests added, still needs final check and info/comments added
* gatk4 version changed to gatk4=4.2.0.0
* multiple sample support added, information added to module yaml file
* Update meta.yml
fixed linting error
* add keywords to meta.yml
* Corrections made to meta.yml
* removed whitespace from meta.yml
Co-authored-by: Gavin.Mackenzie <gavin.mackenzie@nibsc.org>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
