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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align_bowtie2	Subworkflow Infrastructure (#662)	2021-10-08 16:02:42 +01:00
bam_sort_samtools	Fix subworkflows seperate from modules (#933)	2021-11-15 18:18:46 +00:00
bam_stats_samtools	Update to allow cram + update needed to use the gatk4 modules in sarek (#976)	2021-10-29 13:01:05 +02:00
gatk_create_som_pon	feat: fastaidx -> fai (#1073)	2021-11-15 18:03:02 +01:00
gatk_tumor_normal_somatic_variant_calling	Add gatk somatic paired calling subworkflow (#1067)	2021-11-17 11:34:07 +01:00
gatk_tumor_only_somatic_variant_calling	Add gatk somatic tumour calling subworkflow (#1064)	2021-11-17 11:07:17 +01:00
sra_fastq	feat: add sub-workflow for SRA (#836)	2021-10-14 11:50:31 +02:00