GCJMackenzie 08db860938 Update mergebam syntax and sample specific unmapped channel (#1238) ... * 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 * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * updated to follow the new mergebam syntax, also made unaligned input sample specific Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>		2022-01-27 15:30:27 +00:00
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main.nf	Update mergebam syntax and sample specific unmapped channel (#1238)	2022-01-27 15:30:27 +00:00
nextflow.config	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00
test.yml	Update all modules to new NF DSL2 syntax (#1099)	2021-11-26 07:58:40 +00:00