删除 'tasks/CNVkit.wdl'

tasks/CNVkit.wdl

@@ -1,108 +0,0 @@
-task CNVkit {
-  
-  String sample
-  File ref_dir
-  String fasta
-  File ref_flat
-  File regions
-  File hrd
-  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 access ${ref_dir}/${fasta} -o access.bed
-    # Prepare the target bed
-    cnvkit.py target ${regions} --annotate ${ref_flat} --split --short-names -o my_baits.bed
-    if [ ${normal_bam} ]; then
-      cnvkit.py autobin ${tumor_bam} ${normal_bam} -t my_baits.bed -g access.bed
-    else
-      cnvkit.py autobin ${tumor_bam} -t my_baits.bed -g access.bed
-    fi
-    
-    # For each sample...
-    cnvkit.py coverage ${tumor_bam} my_baits.target.bed -o ${sample}.T.targetcoverage.cnn
-    cnvkit.py coverage ${tumor_bam} my_baits.antitarget.bed -o ${sample}.T.antitargetcoverage.cnn
-    if [ ${normal_bam} ]; then
-      cnvkit.py coverage ${normal_bam} my_baits.target.bed -o ${sample}.N.targetcoverage.cnn
-      cnvkit.py coverage ${normal_bam} my_baits.antitarget.bed -o ${sample}.N.antitargetcoverage.cnn
-      # With paired or pooled normals
-      cnvkit.py reference *.N.{,anti}targetcoverage.cnn --fasta ${ref_dir}/${fasta} -o reference.cnn
-    else
-      # With no control sample
-      cnvkit.py reference -o reference.cnn -f ${ref_dir}/${fasta} -t my_baits.target.bed -a my_baits.antitarget.bed
-    fi
-    
-    # For each tumor sample...
-    cnvkit.py fix ${sample}.T.targetcoverage.cnn ${sample}.T.antitargetcoverage.cnn reference.cnn -o ${sample}.cnr
-    cnvkit.py segment ${sample}.cnr -o ${sample}.cns
-    
-    # Check noise
-    cnvkit.py metrics ${sample}.cnr -s ${sample}.cns > ${sample}.stats
-    
-    # Derive each segment's absolute integer copy number, ploidy must be int value
-    PURITY=`awk -F'\t' '{print $6}' ${hrd} | sed -n '2p'`
-    cnvkit.py segmetrics ${sample}.cnr -s ${sample}.cns --ci -o ${sample}.segmetrics.cns
-    cnvkit.py call ${sample}.segmetrics.cns --drop-low-coverage --filter ci -m threshold --purity $PURITY -o ${sample}.call.cns
-    
-    # Plot the results
-    cnvkit.py scatter ${sample}.cnr -s ${sample}.call.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
-    
-    # Genemetrics
-    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
-    # Filter genes
-    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
-    
-    # # Scatter plot for each gene
-    # mkdir gainloss
-    # touch failed_genes.txt
-    # for gene in `cat ${sample}.trusted_genes.txt`
-    # do
-    #   cnvkit.py scatter ${sample}.cnr -s ${sample}.call.cns -g $gene -o ./gainloss/${sample}.$gene.scatter.pdf || echo $gene >> failed_genes.txt
-    # done
-    
-    # Filter by trusted_genes
-    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
-    # Infer absolute CN (not adjust by purity)
-    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 > ${sample}.ratio_cnv.call.filter.txt
-  >>>
-  
-  runtime {
-    docker: docker
-    cluster: cluster_config
-    systemDisk: "cloud_ssd 40"
-    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-  }
-  
-  output {
-    File scatter_pdf = "${sample}.scatter.pdf"
-    File diagram_pdf = "${sample}.diagram.pdf"
-    File heatmap_pdf = "${sample}.heatmap.pdf"
-    File cnr = "${sample}.cnr"
-    File cns = "${sample}.cns"
-    File stats = "${sample}.stats"
-    File call_cns = "${sample}.call.cns"
-    File ratio_cnv = "${sample}.ratio_cnv.txt"
-    File segment_cnv = "${sample}.segment_cnv.txt"
-    File trusted_genes = "${sample}.trusted_genes.txt"
-    File? failed_genes = "${sample}.failed_genes.txt"
-    Array[File]? gainloss = glob("./gainloss/*")
-    File ratio_cnv_trusted = "${sample}.ratio_cnv.trusted.txt"
-    File ratio_cnv_trusted_call = "${sample}.ratio_cnv.call.txt"
-    File ratio_cnv_trusted_call_filter = "${sample}.ratio_cnv.call.filter.txt"
-  }
-}