添加 'tasks/HRD.wdl'

tasks/HRD.wdl

@@ -0,0 +1,67 @@
+task HRD {
+  
+  String sample
+  File ref_dir
+  String fasta
+  File gc
+  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=$(nproc)
+    
+    seqz=${sample}'.seqz.gz'
+    small=${sample}'.small.seqz.gz'
+    
+    # bam2seqz
+    sequenza-utils bam2seqz -gc ${gc} --fasta ${ref_dir}/${fasta} -n ${normal_bam} -t ${tumor_bam} -o $seqz -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY --parallel 24
+    
+    # merge and remove
+    zcat ${sample}_*.seqz.gz | awk '{if (NR == 1 || (NR != 1 && $1 != "chromosome")) {print $0}}' | bgzip > $seqz
+    tabix -f -s 1 -b 2 -e 2 -S 1 $seqz
+    rm ${sample}_*.seqz.gz; rm ${sample}_*.seqz.gz.tbi
+    
+    # seqz_binning: WES: 50; WGS: 200
+    sequenza-utils seqz_binning --seqz $seqz -w 50 -o $small
+    
+    # analysis in r
+    Rscript /home/sequenza/sequenza.r '.' ${sample}
+  >>>
+  
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+  
+  output {
+    File hrd="${sample}.HRD.txt"
+    File alternative_fit="${sample}_alternative_fit.pdf"
+    File alternative_solutions="${sample}_alternative_solutions.txt"
+    File chromosome_depths="${sample}_chromosome_depths.pdf"
+    File chromosome_view="${sample}_chromosome_view.pdf"
+    File CN_bars="${sample}_CN_bars.pdf"
+    File confints_CP="${sample}_confints_CP.txt"
+    File contours_CP="${sample}_contours_CP.pdf"
+    File CP_contours="${sample}_CP_contours.pdf"
+    File gc_plots="${sample}_gc_plots.pdf"
+    File genome_view="${sample}_genome_view.pdf"
+    File model_fit="${sample}_model_fit.pdf"
+    File mutations="${sample}_mutations.txt"
+    File scarHRD_input="${sample}_scarHRD_input.txt"
+    File segments="${sample}_segments.txt"
+    File sequenza_cp_table="${sample}_sequenza_cp_table.RData"
+    File sequenza_extract="${sample}_sequenza_extract.RData"
+    File sequenza_log="${sample}_sequenza_log.txt"
+    File small_seqz="${sample}.small.seqz.gz"
+    File small_seqz_index="${sample}.small.seqz.gz.tbi"
+  }
+}