millironx/nf-core_modules
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3 commits

Author SHA1 Message Date
GCJMackenzie
71945a5b5f
Mutect2 add mitochondria mode and update tests (#967) 
* 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>
 2021-10-29 11:27:56 +01:00
GCJMackenzie
3c4eaec52b
Update for mutect2: add output channel for stats file (#716) 
* 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>
 2021-09-17 09:56:56 +01:00
GCJMackenzie
bd68797ffb
Mutect2 (#682) 
* 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>
 2021-09-13 16:16:23 +01:00