first-commit

inputSamplesFileExamples.csv

+oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam   oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/43061775-40e6-47e7-8f07-b961b44c596f/call-samtools/GCCACATA_S9_L001_R1_001.sorted.bam.bai  
+oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam oss://choppy-cromwell-result/test-choppy/iseq_150pe_rnaseq_20200221_wangshangzi/49bd025e-5275-4fbd-9e67-b279b08ce8b5/call-samtools/F1_S6_L001_R1_001.sorted.bam.bai

inputs

+{
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ bed_file }}".bed_file: "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", 
+  "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.bedtools.disk_size": "100"
+}

tasks/bedtools.wdl

+task multiqc {
+
+	File bam
+	File bai
+	File bed_file
+
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		
+		bedtools multicov -bams ${bam} -bed ${bed_file} > revread_count.txt 
+	
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File multiqc_html = "multiqc_report.html"
+		Array[File] multiqc_txt = glob("multiqc_data/*")
+	}
+}

workflow.wdl

+import "./tasks/bedtools.wdl" as bedtools
+
+workflow {{ project_name }} {
+
+	File inputSamplesFile
+	File bed_file
+	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+
+	scatter (sample in inputSamples) {
+
+		call bedtools.bedtools as bedtools {
+			input:
+			bam=sample[0],
+			bai=sample[1],
+			bed_file=bed_file
+
+		}
+	}
+}
+