From 4e56f2fdbb6f9cca30ae2c12755fcae82960b4b7 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Mon, 15 Jun 2020 21:54:19 +0000 Subject: [PATCH] updating yml Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- yml/bwa-gatk-report-wf-UK.yml | 6 ++++++ yml/gather-vcf.yml | 15 +++------------ yml/getgvcfs.yml | 3 +++ 3 files changed, 12 insertions(+), 12 deletions(-) create mode 100644 yml/getgvcfs.yml diff --git a/yml/bwa-gatk-report-wf-UK.yml b/yml/bwa-gatk-report-wf-UK.yml index 1dfba16..074d16a 100644 --- a/yml/bwa-gatk-report-wf-UK.yml +++ b/yml/bwa-gatk-report-wf-UK.yml @@ -27,3 +27,9 @@ headhtml: tailhtml: class: File location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html + +scattercount: '32' + +knownsites: + class: File + location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz diff --git a/yml/gather-vcf.yml b/yml/gather-vcf.yml index 779a97c..ca2a051 100644 --- a/yml/gather-vcf.yml +++ b/yml/gather-vcf.yml @@ -2,16 +2,7 @@ reference: class: File location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa sample: ERR1726424 -gvcflist: - class: File - location: /data-sdd/pgp/arvados-tutorial/src/variantcalling/sample-files.list -gvcf1: - class: File - location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf.gz - -gvcf2: - class: File - location: keep:dec5da8ebcda12b3eece8705a4391f55+2510/ERR1726424.gatk.g.vcf_10.gz - - +gvcfdir: + class: Directory + location: keep:1da945b644da2182d010fb1b7745233f+2725 diff --git a/yml/getgvcfs.yml b/yml/getgvcfs.yml new file mode 100644 index 0000000..1c646ee --- /dev/null +++ b/yml/getgvcfs.yml @@ -0,0 +1,3 @@ +gvcfdir: + class: Directory + location: keep:1da945b644da2182d010fb1b7745233f+2725 -- 2.30.2