添加 'tasks/fastqscreen.wdl'

tasks/fastqscreen.wdl

@@ -0,0 +1,40 @@
+task fastq_screen {
+  
+  String sample
+  File read1
+  File read2
+  File screen_ref_dir
+  File fastq_screen_conf
+
+  String docker
+  String cluster_config
+  String disk_size
+
+  command <<<
+    set -o pipefail
+    set -e
+    nt=$(nproc)
+    mkdir -p /cromwell_root/tmp
+    cp -r ${screen_ref_dir} /cromwell_root/tmp/
+    ln -s ${read1} ${sample}_R1.fastq.gz
+    ln -s ${read2} ${sample}_R2.fastq.gz
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R1.fastq.gz
+    fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${sample}_R2.fastq.gz
+  >>>
+
+  runtime {
+    docker:docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
+
+  output {
+    File png1 = "${sample}_R1_screen.png"
+    File txt1 = "${sample}_R1_screen.txt"
+    File html1 = "${sample}_R1_screen.html"
+    File png2 = "${sample}_R2_screen.png"
+    File txt2 = "${sample}_R2_screen.txt"
+    File html2 = "${sample}_R2_screen.html"
+  }
+}