From 3872cee6530006b66c7dc47067827577c9b95ad1 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Tue, 21 Apr 2020 01:32:04 +0000
Subject: [PATCH] updating yml to include UK pgp example
 Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com> no issue #

---
 yml/bwa-gatk-report-wf-UK.yml | 29 +++++++++++++++++++++++++++++
 yml/check-sam.yml             |  7 +++++++
 yml/mark-duplicates.yml       |  3 +++
 3 files changed, 39 insertions(+)
 create mode 100644 yml/bwa-gatk-report-wf-UK.yml
 create mode 100644 yml/check-sam.yml
 create mode 100644 yml/mark-duplicates.yml

diff --git a/yml/bwa-gatk-report-wf-UK.yml b/yml/bwa-gatk-report-wf-UK.yml
new file mode 100644
index 0000000..1dfba16
--- /dev/null
+++ b/yml/bwa-gatk-report-wf-UK.yml
@@ -0,0 +1,29 @@
+sample: ERR1726424
+
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
+fastq1:
+  class: File
+  location: keep:c96565a96cd428fe92bf70e97488bd80+21857/ERR1726424_1.fastq/ERR1726424_1.fastq.gz 
+
+fastq2:
+  class: File
+  location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
+
+clinvarvcf:
+  class: File
+  location: keep:242ba3b9049aee86ab2c72db4f3b2822+223/38/clinvar.vcf.gz
+
+reportfunc:
+  class: File
+  location: ../src/annotation/generatereport.py
+
+headhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/head.html
+
+tailhtml:
+  class: File
+  location: /data-sdd/pgp/arvados-tutorial/src/annotation/tail.html
diff --git a/yml/check-sam.yml b/yml/check-sam.yml
new file mode 100644
index 0000000..e87a841
--- /dev/null
+++ b/yml/check-sam.yml
@@ -0,0 +1,7 @@
+sam:
+  class: File
+  location: keep:147b9da57ceb51de9d653e870d8c019a+712/hu297A5D_AE2CH6SK4DG.bam
+
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
diff --git a/yml/mark-duplicates.yml b/yml/mark-duplicates.yml
new file mode 100644
index 0000000..5e68b88
--- /dev/null
+++ b/yml/mark-duplicates.yml
@@ -0,0 +1,3 @@
+bam:
+  class: File
+  location: keep:713b093318f16861084d17a252eef710+12715/WGC069888D.bam
-- 
2.30.2