上传文件至 'tasks'

tasks/CNVkit.wdl

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+
+task cnvkit{
+    String sample
+    File ref_dir
+    String fasta
+    File ref_flat
+    File tumor_bam
+    File tumor_bam_index
+    File? normal_bam
+    File? normal_bam_index
+    String docker
+    String cluster_config
+    String disk_size
+
+    command <<
+        set -o pipefail
+        set -e
+        nt=$(nproc)
+
+        cnvkit.py batch ${tumor_bam} \
+        -n ${normal_bam} \
+        -m wgs \
+        -f ${fasta} \
+        --annotate ${ref_flat}
+
+        cnvkit.py scatter ${sample}.cnr \
+        -s ${sample}.cns \
+        -o ${sample}_scatter.pdf
+
+        cnvkit.py diagram ${sample}.cnr \
+        -s ${sample}.call.cns \
+        -o ${sample}.diagram.pdf
+
+        cnvkit.py heatmap ${sample}.cnr ${sample}.call.cns \
+        -o ${sample}.heatmap.pdf
+
+        cnvkit.py genemetrics ${sample}.cnr -t 0.2 -m 3 -o ${sample}.ratio_cnv.txt
+
+        cnvkit.py genemetrics ${sample}.cnr -s ${sample}.call.cns -t 0.2 -m 3 -o ${sample}.segment_cnv.txt
+
+        cat WGS_IL_T_1.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 WGS_IL_T_1.ratio_cnv.txt > ${sample}.ratio_cnv.trusted.txt
+        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
+
+        ls ./
+
+        tar cvf ${sample}.tar ./
+
+    >>
+
+    runtime{
+        docker:docker
+        cluster:cluster_config
+        systemDisk:"cloud_ssd 40"
+        dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output{
+        File out_file = "${sample}.tar"
+    }
+
+}