Francesco L a68c563e54 Added UMI sub-workflow (#1098) ... * added code for subworkflow fgbio call umi consensus * ironing out a few typos etc * fixing last things * fixed md5sum - lets see if it changes * removing file accidentally deleted * tidy indents * added bwamem2 alternative * fixed entry for both tests * changed name second test workflow entry * fixed workflow entry names * fixed md5sum for file generated with bwamem2 * added syntax new DSL2 * added new config location in test command line * added new config location in test command line * use of prefix instead of suffix because modules have been changed in this way * explicit alias to bwa mem1 to avoid confusion * removed param that should be an ext optional argument in fgbio groupreadsbyumi * missing colon in config * missing colon in module config too * order list alphabetically Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * remove params from body Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * improving readability of input structure Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> * reverting to mandatory input * fixed tests and workflow take values * remove param Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * simplify tests params Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * formatting inputs for readability * factoring in changes to bwamem2_mem and bwa_mem sort/view inputs * updating test md5sum for grouped file following code update in bwamem Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>		2021-12-09 11:16:40 +01:00
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align_bowtie2	Subworkflow Infrastructure (#662)	2021-10-08 16:02:42 +01:00
annotation_ensemblvep	Add subworkflows for ensemblvep and snpeff (#1124)	2021-12-07 17:12:35 +01:00
annotation_snpeff	Add subworkflows for ensemblvep and snpeff (#1124)	2021-12-07 17:12:35 +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
fgbio_create_umi_consensus	Added UMI sub-workflow (#1098)	2021-12-09 11:16:40 +01:00
gatk_create_som_pon	use underscores in anchors and references (#1080)	2021-11-18 18:09:09 +00:00
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