删除 'tasks/multiqc.wdl'

tasks/multiqc.wdl

-task multiqc {
-
-	Array[File] read1_zip
-	Array[File] read2_zip
-
-	Array[File] txt1
-	Array[File] txt2
-
-	Array[File] bamqc_zip
-	Array[File] rnaseq_zip
-
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e
-		mkdir -p /cromwell_root/tmp/fastqc
-		mkdir -p /cromwell_root/tmp/fastqscreen
-		mkdir -p /cromwell_root/tmp/bamqc
-		mkdir -p /cromwell_root/tmp/rnaseq
-
-		cp ${sep=" " read1_zip} ${sep=" " read2_zip} /cromwell_root/tmp/fastqc
-		cp ${sep=" " txt1} ${sep=" " txt2} /cromwell_root/tmp/fastqscreen
-		for i in ${sep=" " bamqc_zip}
-		do
-		  tar -zxvf $i -C /cromwell_root/tmp/bamqc
-		done
-		
-		for i in ${sep=" " rnaseq_zip}
-		do
-		  tar -zxvf $i -C /cromwell_root/tmp/rnaseq
-		done
-		
-
-		multiqc /cromwell_root/tmp/
-		cat multiqc_data/multiqc_fastq_screen.txt > multiqc_fastq_screen.txt
-		cat multiqc_data/multiqc_fastqc.txt > multiqc_fastqc.txt
-		cat multiqc_data/multiqc_general_stats.txt > multiqc_general_stats.txt
-		cat multiqc_data/multiqc_qualimap_bamqc_genome_results.txt > multiqc_qualimap_bamqc_genome_results.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/*")
-		File multiqc_fastq_screen = "multiqc_fastq_screen.txt"
-		File multiqc_fastqc = "multiqc_fastqc.txt"
-		File multiqc_general_stats = "multiqc_general_stats.txt"
-		File bamqc_genome_results = "multiqc_qualimap_bamqc_genome_results.txt"
-	}
-}