更新 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -0,0 +1,64 @@
+
+task cnvkit{
+    String sample_id
+    File ref_dir
+    String? fasta
+    File ref_flat
+    # File hrd
+    File tumor_bam
+    File tumor_bam_index
+    File? normal_bam
+    File? normal_bam_index
+    String docker
+    String cluster_config
+    String disk_size
+    String sample=basename(tumor_bam,".bam")
+
+    command <<<
+
+        set -o pipefail
+        set -e
+        nt=$(nproc)
+        
+        echo ${sample}
+
+        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} \
+                  --normal ${normal_bam} \
+                  --method wgs \
+                  --fasta ${ref_dir} \
+                  --annotate ${ref_flat} -p $nt \
+                  --drop-low-coverage \
+                  --output-dir ${sample}.reference.cnn
+        
+       /root/miniconda2/bin/cnvkit.py batch  ${tumor_bam} \
+                  -r ${sample}.reference.cnn \
+                  --output-dir ${sample}.sampleid.cns \
+                  -p $nt
+                  
+                  
+       /root/miniconda2/bin/cnvkit.py call ${sample}.sampleid.cns \
+                  -o ${sample}.sampleid.call.cns
+                  
+        
+                  
+
+        ls ./
+
+        tar cvf ${sample}.tar ${sample}*
+
+    >>>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+        timeout:259200
+    }
+
+    output{
+        File out_file = "${sample}.tar"
+        #File cnv_bed = "${sample}.ratio_cnv.call.filter.bed"
+    }
+
+}

tasks/CNVkit_test.wdl

@@ -1,77 +0,0 @@
-
-task cnvkit{
-    String sample_id
-    File ref_dir
-    String? fasta
-    File ref_flat
-    # File hrd
-    File tumor_bam
-    File tumor_bam_index
-    File? normal_bam
-    File? normal_bam_index
-    String docker
-    String cluster_config
-    String disk_size
-    String sample=basename(tumor_bam,".bam")
-
-    command <<<
-
-        set -o pipefail
-        set -e
-        nt=$(nproc)
-        
-        echo ${sample}
-
-        /root/miniconda2/bin/cnvkit.py batch ${tumor_bam} -n ${normal_bam} -m wgs -f ${ref_dir} --annotate ${ref_flat} -p $nt
-
-                  
-        # Check noise
-    	/root/miniconda2/bin/cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
-    
-        # Derive each segment's absolute integer copy number, ploidy must be int value
-        PURITY=0.3
-        /root/miniconda2/bin/cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns
-        /root/miniconda2/bin/cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns
-          
-
-        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
-
-        /root/miniconda2/bin/cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
-
-
-        /root/miniconda2/bin/cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -o ${sample}_scatter.pdf
-
-        /root/miniconda2/bin/cnvkit.py diagram ${sample}.cnr -s ${sample}.call.cns -o ${sample}.diagram.pdf
-
-        /root/miniconda2/bin/cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns -o ${sample}.heatmap.pdf
-
-        cat ${sample}.ratio_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > ratio_cnv.txt
-        cat ${sample}.segment_cnv.txt | tail -n+2 | cut -f1 | sort | uniq > segment_cnv.txt
-        comm -12 ratio_cnv.txt segment_cnv.txt > ${sample}.trusted_genes.txt
-
-        awk 'NR==FNR {a[$1]=$2;next} NR!=FNR {if(FNR == 1 || (FNR != 1 && $1 in a)) print $0}' ${sample}.trusted_genes.txt ${sample}.ratio_cnv.txt > ${sample}.ratio_cnv.trusted.txt
-        /root/miniconda2/bin/cnvkit.py call ${sample}.ratio_cnv.trusted.txt -m threshold -o ${sample}.ratio_cnv.call.txt
-        awk '{if ($6 != 2) print $0}' ${sample}.ratio_cnv.call.txt > ${sample}.ratio_cnv.call.filter.txt
-        
-        cp ${sample}.ratio_cnv.call.filter.txt ${sample}.ratio_cnv.call.filter.bed
-
-        ls ./
-
-        tar cvf ${sample}.tar ${sample}*
-
-    >>>
-
-    runtime{
-        docker:docker
-        cluster:cluster_config
-        systemDisk:"cloud_ssd 40"
-        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
-        timeout:259200
-    }
-
-    output{
-        File out_file = "${sample}.tar"
-        File cnv_bed = "${sample}.ratio_cnv.call.filter.bed"
-    }
-
-}