filter

tasks/Freebayes.wdl

@@ -3,9 +3,9 @@ task Freebayes {
     File ref_dir
     File ref_fa_fai
 	File fasta
-
 	File Dedup_bam
 	File Dedup_bam_index
+	String half_read_length
 	String sample
 	String FBdocker
 	String cluster_config
@@ -15,7 +15,9 @@ task Freebayes {
 		set -o pipefail
 		set -e	
 		nt=$(nproc)
-		/opt/freebayes/scripts/freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100000) $nt -f ${ref_dir}/${fasta} --genotype-qualities --max-complex-gap 75 ${Dedup_bam} > ${sample}_fb.vcf
+		/opt/freebayes/scripts/freebayes-parallel <(/opt/freebayes/scripts/fasta_generate_regions.py ${ref_dir}/${ref_fa_fai} 100000) $nt -f ${ref_dir}/${fasta} --genotype-qualities -F 0.05 --max-complex-gap ${half_read_length} ${Dedup_bam} > ${sample}_fb.vcf
+		cat ${sample}_fb.vcf | grep '#' > header
+		cat ${sample}_fb.vcf | grep -v '#' | grep -v '0/0' | cat header - > ${sample}_fb.filtered.vcf
 	>>>
 
 	runtime {
@@ -26,5 +28,6 @@ task Freebayes {
 	}
 	output {
 		File vcf = "${sample}_fb.vcf"
+		File filtered = "${sample}_fb.filtered.vcf"
 	}
 }

workflow.wdl

@@ -1,7 +1,7 @@
 import "./tasks/Freebayes.wdl" as Freebayes
 
 
-workflow {{ project_name }} {
+workflow project_name {
 
 	String sample
 	String FBdocker
@@ -10,6 +10,7 @@ workflow {{ project_name }} {
 	File Dedup_bam
 	File Dedup_bam_index
 	File ref_dir
+	String half_read_length
 	String disk_size
 	String cluster_config
 
@@ -20,6 +21,7 @@ workflow {{ project_name }} {
 		Dedup_bam=Dedup_bam,
 		Dedup_bam_index=Dedup_bam_index,
 		sample=sample,
+		half_read_length=half_read_length,
 		FBdocker=FBdocker,
 		cluster_config=cluster_config,
 		disk_size=disk_size,