From a1cfc790f2bcce7ab764319ec9772755bcc1b747 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Wed, 1 Jul 2020 18:59:02 +0000 Subject: [PATCH] Switching variable knownsites1 to knownsites in yml files Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- .../yml/helper/gatk-baserecalibrator-with-interval.yml | 2 +- WGS-processing/yml/helper/gatk-wf-with-interval.yml | 6 +++++- WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml index 7e6b16a..d22173f 100644 --- a/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml +++ b/WGS-processing/yml/helper/gatk-baserecalibrator-with-interval.yml @@ -8,7 +8,7 @@ reference: sample: ERR1726424 -knownsites1: +knownsites: class: File location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz diff --git a/WGS-processing/yml/helper/gatk-wf-with-interval.yml b/WGS-processing/yml/helper/gatk-wf-with-interval.yml index 5761d1d..e1e2b94 100644 --- a/WGS-processing/yml/helper/gatk-wf-with-interval.yml +++ b/WGS-processing/yml/helper/gatk-wf-with-interval.yml @@ -1,13 +1,17 @@ bam: class: File location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam + reference: class: File location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa + intervallist: class: File location: keep:4d4947f6637f0acec32580e09d991967+815/0000-scattered.interval_list + sample: ERR1726424 -knownsites1: + +knownsites: class: File location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz diff --git a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml index f6d4943..4a36ecb 100644 --- a/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml +++ b/WGS-processing/yml/helper/scatter-gatk-wf-with-interval.yml @@ -10,6 +10,6 @@ sample: ERR1726424 scattercount: '32' -knownsites1: +knownsites: class: File location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz -- 2.30.2