GCJMackenzie 5b975cc20d Add gatk somatic paired calling subworkflow (#1067) ... * initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * tests should now work after the yml update * Update pytest_modules.yml Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>		2021-11-17 11:34:07 +01:00
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nextflow.config	Remove docker.runOptions in favor of docker.userEmulation. (#525)	2021-05-27 18:29:17 +01:00
pytest_modules.yml	Add gatk somatic paired calling subworkflow (#1067)	2021-11-17 11:34:07 +01:00
test_data.config	Cooler cload (#634)	2021-11-15 21:43:55 +00:00