GCJMackenzie 071b1d50a8 Add gatk somatic tumour calling subworkflow (#1064) ... * initial commit to set up new branch * save changes to checkout * workflow working, still needs test.yml and meta.yml, also fix versions file * subworkflow finished * Update pytest_subworkflows.yml * Update pytest_subworkflows.yml * Update pytest_subworkflows.yml * fix config subworkflow name * Update main.nf * Update pytest_subworkflows.yml * fixed md5sum issue likely caused by gatk version update * tumour changed to tumor * old dir deleted * Comments added to explain use of placeholders '[]' * updated index names, input channel renamed to input * Apply suggestions from code review * updated to perform new subworkflow testing Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>		2021-11-17 11:07:17 +01:00
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align_bowtie2	Fix subworkflows seperate from modules (#933)	2021-11-15 18:18:46 +00:00
bam_sort_samtools	Fix subworkflows seperate from modules (#933)	2021-11-15 18:18:46 +00:00
bam_stats_samtools	Subworkflow Infrastructure (#662)	2021-10-08 16:02:42 +01:00
gatk_create_som_pon	Fix subworkflows seperate from modules (#933)	2021-11-15 18:18:46 +00:00
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