adding base recalibrator yml and updating bwamem yml

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

diff --git a/yml/bwamem-samtools-sort.yml b/yml/bwamem-samtools-sort.yml
new file mode 100644 (file)
index 0000000..91e5357
--- /dev/null
+++ b/yml/bwamem-samtools-sort.yml
@@ -0,0 +1,10 @@
+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/yml/bwamem-samtools-view.yml b/yml/bwamem-samtools-view.yml
index 24f4eb419ac4404f99e050bdc41f9cc21783a80a..91e5357f8c4a7035231b9f502021da6bb099b27b 100644 (file)
--- a/yml/bwamem-samtools-view.yml
+++ b/yml/bwamem-samtools-view.yml
@@ -3,8 +3,8 @@ reference:
   location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
 fastq1:
   class: File
-  location: ../../bam/hu297A5D_AE2CH6SK4DG-EXT_100000_R1.fastq.gz
+  location: keep:c96565a96cd428fe92bf70e97488bd80+21857/ERR1726424_1.fastq/ERR1726424_1.fastq.gz  
 fastq2:
   class: File
-  location: ../../bam/hu297A5D_AE2CH6SK4DG-EXT_100000_R2.fastq.gz
-
+  location: keep:0ea6e3aaa6ead18a2cc4ba67a22939e9+25007/ERR1726424_2.fastq/ERR1726424_2.fastq.gz
+sample: ERR1726424

diff --git a/yml/gatk-baserecalibrator.yml b/yml/gatk-baserecalibrator.yml
new file mode 100644 (file)
index 0000000..d4b3c50
--- /dev/null
+++ b/yml/gatk-baserecalibrator.yml
@@ -0,0 +1,14 @@
+bam:
+  class: File
+  location: keep:79407f4f0d46a44fcc9c377461ee85fc+53752/marked_dupsERR1726424.sorted.bam
+
+reference:
+  class: File
+  location: keep:a3af04432df3d71d22f2fe8be549ba96+5974/hg38.fa
+
+sample: ERR1726424
+
+knownsites1:
+  class: File
+  location: keep:7c0b13bda857fa15d88c1039182f69d5+8052/Homo_sapiens_assembly38.known_indels.vcf.gz
+