first commit

inputSamplesFileExamples.tsv

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+oss://choppy-cromwell-result/test-choppy/RNAseq_0p5M_20200209/30523014-5772-4bdc-b3b9-d6688a152573/call-samtools/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_F7_3_20190710_CleanData_R1_0.sorted.bam	oss://choppy-cromwell-result/test-choppy/RNAseq_0p5M_20200209/30523014-5772-4bdc-b3b9-d6688a152573/call-samtools/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_F7_3_20190710_CleanData_R1_0.sorted.bam.bai
+oss://choppy-cromwell-result/test-choppy/RNAseq_0p5M_20200209/4302d90f-1a84-40a1-8f56-99bb3652fade/call-samtools/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_F7_1_20190710_CleanData_R1_0.sorted.bam	oss://choppy-cromwell-result/test-choppy/RNAseq_0p5M_20200209/4302d90f-1a84-40a1-8f56-99bb3652fade/call-samtools/Quartet_RNA_ILM_NovaSeq_RiboZero_FDU_F7_1_20190710_CleanData_R1_0.sorted.bam.bai
+oss://choppy-cromwell-result/test-choppy/RNAseq_0p5M_20200209/76162f0f-e580-4a1b-8932-33ea5dad9ba3/call-samtools/Quartet_RNA_ILM_HiSeq4000_RiboZero_UTS_BLD8_1_20161209_CleanData_R1_0.sorted.bam	oss://choppy-cromwell-result/test-choppy/RNAseq_0p5M_20200209/76162f0f-e580-4a1b-8932-33ea5dad9ba3/call-samtools/Quartet_RNA_ILM_HiSeq4000_RiboZero_UTS_BLD8_1_20161209_CleanData_R1_0.sorted.bam.bai

inputs

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+{
+  "{{ project_name }}.qualimapBAMqc.disk_size": "500",
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ project_name }}.multiqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
+  "{{ project_name }}.qualimapBAMqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+  "{{ project_name }}.qualimapBAMqc.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+  "{{ project_name }}.multiqc.disk_size": 100"
+}

tasks/multiqc.wdl

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+task multiqc {
+
+	Array[File] bamqc_zip
+
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		mkdir -p /cromwell_root/tmp/bamqc
+
+		for i in ${sep=" " bamqc_zip}
+		do
+		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
+		done
+
+		multiqc /cromwell_root/tmp/
+	
+	>>>
+
+	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/*")
+	}
+}

tasks/qualimapBAMqc.wdl

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+task qualimapBAMqc {
+	File bam
+	File bai
+	String bamname = basename(bam,".bam")
+	String docker
+	String cluster_config
+	String disk_size
+
+	command <<<
+		set -o pipefail
+		set -e
+		nt=$(nproc)
+		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
+		tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
+	>>>
+
+	runtime {
+		docker:docker
+		cluster:cluster_config
+		systemDisk:"cloud_ssd 40"
+		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
+	}
+}

workflow.wdl

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