Added exclude.txt to exclude bad samples from the joint genotyping.

Author: eanokian

Dockstore.cwl

@@ -27,7 +27,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/zek12/dockerized_gatk_pipeline:0.1.0"
+    dockerPull: "quay.io/zek12/dockerized_gatk_pipeline:0.2.0"
 
 hints:
   - class: ResourceRequirement
@@ -67,6 +67,13 @@ inputs:
       position: 4
       shellQuote: true
 
+  exclude:
+    type: File
+    doc: "A txt file with the gvcfs to exclude (bad samples) from the joint genotyping. Samples have to be one per line and ending with .g.vcf.gz"
+    inputBinding:
+      position: 5
+      shellQuote: true
+
 
 outputs:
 

Dockstore.json

@@ -9,8 +9,12 @@
     "path": "http://ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz",
     "class": "File"
   },
+  "exclude": {
+    "path": "exclude.txt",
+    "class": "File"
+  },
   "vcf": {
-    "path": "/tmp/joint_chrY.vcf",
+    "path": "joint_chrY.vcf",
     "class": "File"
   }
 }

exclude.txt

@@ -0,0 +1,2 @@
+sample1.g.vcf.gz
+sample2.g.vcf.gz

scripts/part3_joint_genotyping.sh

@@ -15,11 +15,20 @@ path_logs="."
 path_output_vcf="."
 mem=$3 # = 32
 ref_genome=$4
+exclude=$5
+
+# remove last slash in input dirs if they end with slash
+path_to_gvcfs=${path_to_gvcfs%/}
+
 
 gatk_ref_bundle_dbsnp="/opt/dbsnp_138.b37.vcf.gz"
 logfile=${path_logs}/log.log
 
 
+# exclude bad samples
+# ls -1a $path_to_gvcfs/*.g.vcf.gz | sed -e 's/.*\///g' | sed -e 's/\..*//g' > all_samples.txt
+ls -1a $path_to_gvcfs/*.g.vcf.gz | sed -e 's/.*\///g' > all_samples.txt
+grep -F -x -v -f $exclude all_samples.txt > passed.txt
 
 
 # prepare ref genome
@@ -47,8 +56,10 @@ if [ ! -f $path_logs/part_3_GenotypeGVCFs_finished_chr$chr.txt ]; then
 
 	echo "$(date '+%d/%m/%y_%H:%M:%S'),---Starting GenotypeGVCFs: joint genotyping of chromosome $chr---" >> "$logfile"
 
-	gvcf_paths=$(ls $path_to_gvcfs/*.g.vcf.gz)
-	gvcf_array=$(for i in $gvcf_paths; do echo "--variant $i"; done)
+	# gvcf_paths=$(ls $path_to_gvcfs/*.g.vcf.gz)
+	# gvcf_array=$(for i in $gvcf_paths; do echo "--variant $i"; done)
+	gvcf_paths=$(cat passed.txt)
+	gvcf_array=$(for i in $gvcf_paths; do echo "--variant $path_to_gvcfs/$i"; done)
 
 	time ($this_gatk \
 	-T GenotypeGVCFs \