revise samtools output

defaults

@@ -20,5 +20,6 @@
     "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
     "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",
     "count_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "insert_size":"8000",
     "count_length": "150"
 }

inputs

@@ -14,6 +14,7 @@
     "{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
     "{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
     "{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
+    "{{ project_name }}.insert_size": "{{ insert_size }}",
     "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
     "{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
     "{{ project_name }}.qualimap_docker": "{{ qualimap_docker }}",

tasks/qualimap.wdl

@@ -11,7 +11,7 @@ task qualimap {
 		set -e
 		nt=$(nproc)
 		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
-		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=32G
+		/opt/qualimap/qualimap rnaseq -bam ${bam_percent} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=32G
 		tar -zcf ${bamname}_bamqc_qualimap.tar.gz ${bamname}_bamqc
 		tar -zcf ${bamname}_rnaseq_qualimap.tar.gz ${bamname}_rnaseq
 		

tasks/samtools.wdl

@@ -4,10 +4,13 @@ task samtools {
     String bam=base + ".bam"
     String sorted_bam=base + ".sorted.bam"
     String sorted_bam_index=base + ".sorted.bam.bai"
+    String percent_bam=base + ".percent.bam"
     String samstats=base + ".samstats"
+    String ins_size=base + ".ins_size" 
     String docker
     String cluster
     String disk_size
+    Int insert_size
 
     command <<<
        set -o pipefail
@@ -15,7 +18,10 @@ task samtools {
        /opt/conda/bin/samtools view -bS ${sam} > ${bam}
        /opt/conda/bin/samtools sort -m 1000000000 ${bam} -o ${sorted_bam}
        /opt/conda/bin/samtools index ${sorted_bam}
+       /opt/conda/bin/samtools view -bs 42.1 ${sorted_bam} > ${percent_bam}
        /opt/conda/bin/samtools stats ${sorted_bam} > ${samstats}
+       /opt/conda/bin/samtools stats -i ${insert_size} ${sorted_bam} |grep ^IS|cut -f 2- > ${ins_size}
+
     >>>
 
     runtime {
@@ -26,9 +32,11 @@ task samtools {
     }
 
     output {
-      File out_sort_bam=sorted_bam
-      File out_sort_bam_index=sorted_bam_index
-      File out_samstats=samstats
+       File out_sort_bam=sorted_bam
+       File out_sort_bam_index=sorted_bam_index
+       File out_percent = percent_bam
+       File out_samstats=samstats
+       File out_ins_size=ins_size
     }
 
 }

workflow.wdl

@@ -27,6 +27,7 @@ workflow {{ project_name }} {
 	String stringtie_cluster
 	String samtools_docker
 	String samtools_cluster
+	Int insert_size
 	String qualimap_docker
 	String qualimap_cluster
 	String ballgown_docker
@@ -78,12 +79,14 @@ workflow {{ project_name }} {
 		docker=samtools_docker,
 		cluster=samtools_cluster,
 		sam=hisat2.sam,
+		insert_size = insert_size,
 		disk_size=disk_size
 		}
 
 	call qualimap.qualimap as qualimap {
 		input:
 		bam=samtools.out_sort_bam,
+		bam_percent=samtools.out_percent	
 		gtf=gtf, 
 		docker=qualimap_docker,
 		cluster=qualimap_cluster,