From f1ea95e8a844ede6d1306b973d4f98b644454d52 Mon Sep 17 00:00:00 2001
From: Sarah Wait Zaranek <swz@curii.com>
Date: Fri, 3 Jul 2020 13:14:45 +0000
Subject: [PATCH] Updating yml files Arvados-DCO-1.1-Signed-off-by: Sarah Wait
 Zaranek <swz@curii.com> no issue #

---
 WGS-processing/yml/helper/bwamem-samtools-sort.yml     | 10 ----------
 .../helper/{gather-array-vcf.yml => gather-vcf.yml}    |  2 ++
 WGS-processing/yml/helper/gatk-haplotypecaller.yml     |  6 ------
 WGS-processing/yml/helper/getgvcfs.yml                 |  3 ---
 WGS-processing/yml/wgs-processing-wf.yml               |  5 +++++
 5 files changed, 7 insertions(+), 19 deletions(-)
 delete mode 100644 WGS-processing/yml/helper/bwamem-samtools-sort.yml
 rename WGS-processing/yml/helper/{gather-array-vcf.yml => gather-vcf.yml} (98%)
 delete mode 100644 WGS-processing/yml/helper/gatk-haplotypecaller.yml
 delete mode 100644 WGS-processing/yml/helper/getgvcfs.yml

diff --git a/WGS-processing/yml/helper/bwamem-samtools-sort.yml b/WGS-processing/yml/helper/bwamem-samtools-sort.yml
deleted file mode 100644
index 91e5357..0000000
--- a/WGS-processing/yml/helper/bwamem-samtools-sort.yml
+++ /dev/null
@@ -1,10 +0,0 @@
-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
-sample: ERR1726424
diff --git a/WGS-processing/yml/helper/gather-array-vcf.yml b/WGS-processing/yml/helper/gather-vcf.yml
similarity index 98%
rename from WGS-processing/yml/helper/gather-array-vcf.yml
rename to WGS-processing/yml/helper/gather-vcf.yml
index ca2a051..e863403 100644
--- a/WGS-processing/yml/helper/gather-array-vcf.yml
+++ b/WGS-processing/yml/helper/gather-vcf.yml
@@ -1,7 +1,9 @@
 reference:
   class: File
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
 sample: ERR1726424
+
 gvcfdir:
   class: Directory
   location: keep:1da945b644da2182d010fb1b7745233f+2725
diff --git a/WGS-processing/yml/helper/gatk-haplotypecaller.yml b/WGS-processing/yml/helper/gatk-haplotypecaller.yml
deleted file mode 100644
index 9aab1b9..0000000
--- a/WGS-processing/yml/helper/gatk-haplotypecaller.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-bam:
-  class: File
-  location: keep:6e574d6e8eb051b5ab2554e088b39332+144/out.sorted.bam
-reference:
-  class: File
-  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
diff --git a/WGS-processing/yml/helper/getgvcfs.yml b/WGS-processing/yml/helper/getgvcfs.yml
deleted file mode 100644
index 1c646ee..0000000
--- a/WGS-processing/yml/helper/getgvcfs.yml
+++ /dev/null
@@ -1,3 +0,0 @@
-gvcfdir:
-  class: Directory 
-  location: keep:1da945b644da2182d010fb1b7745233f+2725
diff --git a/WGS-processing/yml/wgs-processing-wf.yml b/WGS-processing/yml/wgs-processing-wf.yml
index 85b2ffd..f56f8cb 100644
--- a/WGS-processing/yml/wgs-processing-wf.yml
+++ b/WGS-processing/yml/wgs-processing-wf.yml
@@ -1,5 +1,6 @@
 reference:
   class: File
+  format: edam:format_1929
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 
 fastqdir:
@@ -8,6 +9,7 @@ fastqdir:
 
 clinvarvcf:
   class: File
+  format: edam:format_3016
   location: keep:242ba3b9049aee86ab2c72db4f3b2822+223/38/clinvar.vcf.gz
 
 reportfunc:
@@ -16,14 +18,17 @@ reportfunc:
 
 headhtml:
   class: File
+  format: edam:format_2331
   location: ../src/annotation/head.html
 
 tailhtml:
   class: File
+  format: edam:format_2331
   location: ../src/annotation/tail.html
 
 scattercount: '32'
 
 knownsites:
   class: File
+  format: edam:format_3016
   location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
-- 
2.30.2