uniform delimiter

inputs

@@ -22,7 +22,7 @@
     "{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
     "{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
     "{{ project_name }}.count_docker": "{{ count_docker }}",
-	"{{ project_name }}.count_cluster": "{{ count_cluster }}",
-	"{{ project_name }}.count_length": "{{ count_length }}",
+    "{{ project_name }}.count_cluster": "{{ count_cluster }}",
+    "{{ project_name }}.count_length": "{{ count_length }}",
     "{{ project_name }}.pre_alignment_qc": "{{ pre_alignment_qc }}"
 }

tasks/fastqc.wdl

@@ -15,9 +15,9 @@ task fastqc {
 
 	runtime {
 		docker:docker
-    	cluster: cluster
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
 		File read1_html = sub(basename(read1), "\\.(fastq|fq)\\.gz$", "_fastqc.html")

tasks/fastqscreen.wdl

@@ -15,16 +15,16 @@ task fastqscreen {
 		nt=$(nproc)
 		# mkdir -p /cromwell_root/tmp
 		# cp -r ${screen_ref_dir} /cromwell_root/tmp/
-        sed -i "s#/cromwell_root/fastq_screen_reference#${screen_ref_dir}#g" ${fastq_screen_conf}
+		sed -i "s#/cromwell_root/fastq_screen_reference#${screen_ref_dir}#g" ${fastq_screen_conf}
 		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read1}
 		fastq_screen --aligner bowtie2 --conf ${fastq_screen_conf} --top 100000 --threads $nt ${read2}
 	>>>
 
 	runtime {
 		docker:docker
-    	cluster: cluster
-    	systemDisk: "cloud_ssd 40"
-    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+		cluster: cluster
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
 	}
 	output {
 		File png1 = "${read1name}_screen.png"

tasks/hisat2.wdl

@@ -10,15 +10,15 @@ task hisat2 {
    
 
    command {
-     nt=$(nproc)
-     hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam  --un-conc-gz ${base}_un.fq.gz
+      nt=$(nproc)
+      hisat2 -t -p $nt -x ${idx}/${idx_prefix} -1 ${read_1P} -2 ${read_2P} -S ${base}.sam  --un-conc-gz ${base}_un.fq.gz
    }
    
    runtime { 
-		docker: docker 
-		cluster: cluster
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+      docker: docker 
+      cluster: cluster
+      systemDisk: "cloud_ssd 40"
+      dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
    }
 
    output {

tasks/qualimap.wdl

@@ -13,7 +13,7 @@ task qualimap {
 		nt=$(nproc)
 		/opt/qualimap/qualimap rnaseq -bam ${bam} -outformat HTML -outdir ${bamname}_rnaseq -gtf ${gtf} -pe --java-mem-size=10G
 		tar -zcvf ${bamname}_rnaseq_qualimap.zip ${bamname}_rnaseq
-        /opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
+		/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
 	>>>
 
@@ -26,6 +26,6 @@ task qualimap {
 
 	output {
 		File rnaseq_zip = "${bamname}_rnaseq_qualimap.zip"
-        File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
+		File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
 	}
 }

workflow.wdl

@@ -11,16 +11,16 @@ workflow {{ project_name }} {
 
 	File read1
 	File read2
-    File idx
+	File idx
 	File screen_ref_dir
 	File fastq_screen_conf
 	String idx_prefix
-    File gtf
+	File gtf
 	String disk_size
-    String fastqc_docker
-    String fastqc_cluster
+	String fastqc_docker
+	String fastqc_cluster
 	String fastqscreen_docker
-    String fastqscreen_cluster
+	String fastqscreen_cluster
 	String hisat2_docker
 	String hisat2_cluster
 	String stringtie_docker
@@ -67,8 +67,8 @@ workflow {{ project_name }} {
 		disk_size= disk_size
 		}
 
-    call samtools.samtools as samtools {
-        input: 
+	call samtools.samtools as samtools {
+		input: 
 		docker = samtools_docker,
 		cluster = samtools_cluster,
 		sam = hisat2.sam,
@@ -85,8 +85,8 @@ workflow {{ project_name }} {
 		disk_size = disk_size
 		}
 
-    call stringtie.stringtie as stringtie {
-        input: 
+	call stringtie.stringtie as stringtie {
+		input: 
 		docker = stringtie_docker,
 		cluster = stringtie_cluster,
 		gtf = gtf,