Adding yml files for gathering and intervals

Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #

diff --git a/yml/gather-vcf.yml b/yml/gather-vcf.yml
new file mode 100644 (file)
index 0000000..779a97c
--- /dev/null
+++ b/yml/gather-vcf.yml
@@ -0,0 +1,17 @@
+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
+
+
+

diff --git a/yml/gather-vcf2.yml b/yml/gather-vcf2.yml
new file mode 100644 (file)
index 0000000..ce9852f
--- /dev/null
+++ b/yml/gather-vcf2.yml
@@ -0,0 +1,13 @@
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+sample: ERR1726424
+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
+
+

diff --git a/yml/gatk-applyBQSR.yml b/yml/gatk-applyBQSR.yml
new file mode 100644 (file)
index 0000000..0241acd
--- /dev/null
+++ b/yml/gatk-applyBQSR.yml
@@ -0,0 +1,13 @@
+bam:
+  class: File
+  location: keep:79407f4f0d46a44fcc9c377461ee85fc+53752/marked_dupsERR1726424.sorted.bam
+
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
+sample: ERR1726424
+
+recaltable: 
+  class: File
+  location: keep:fdce030a5036edb9b821222e316ee706+143/ERR1726424_recal_data.table

diff --git a/yml/gatk-haplotypecaller-with-interval.yml b/yml/gatk-haplotypecaller-with-interval.yml
new file mode 100644 (file)
index 0000000..4c42573
--- /dev/null
+++ b/yml/gatk-haplotypecaller-with-interval.yml
@@ -0,0 +1,10 @@
+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

diff --git a/yml/gatk-splitintervals.yml b/yml/gatk-splitintervals.yml
new file mode 100644 (file)
index 0000000..68dbcc4
--- /dev/null
+++ b/yml/gatk-splitintervals.yml
@@ -0,0 +1,7 @@
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
+sample: ERR1726424
+
+scattercount: "32"

diff --git a/yml/gatk-wf-with-interval.yml b/yml/gatk-wf-with-interval.yml
new file mode 100644 (file)
index 0000000..5761d1d
--- /dev/null
+++ b/yml/gatk-wf-with-interval.yml
@@ -0,0 +1,13 @@
+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:
+  class: File
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz

diff --git a/yml/scatter-gatk-wf-with-interval.yml b/yml/scatter-gatk-wf-with-interval.yml
new file mode 100644 (file)
index 0000000..4909ce2
--- /dev/null
+++ b/yml/scatter-gatk-wf-with-interval.yml
@@ -0,0 +1,11 @@
+bam:
+  class: File
+  location: keep:377c02de508dff9e4474f9a48d754933+53821/marked_dupsERR1726424.sorted.bam 
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+sample: ERR1726424
+scattercount: '32'
+knownsites1:
+  class: File
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz