revised inputs

inputs

@@ -5,7 +5,7 @@
     "{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
     "{{ project_name }}.idx": "{{ idx }}",
     "{{ project_name }}.gtf": "{{ gtf }}",
-    "{{ project_name }}.disk_size": "{{ disk_size }}",
+    "{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}",
     "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
     "{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
     "{{ project_name }}.fastqscreen_cluster": "{{ fastqscreen_cluster }}",

tasks/qualimap.wdl

@@ -12,7 +12,7 @@ task qualimap {
 		set -e
 		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
+		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 
 		tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
 	>>>
@@ -25,7 +25,7 @@ task qualimap {
 	}
 
 	output {
-		File rnaseq_zip = "${bamname}_RNAseq_qualimap.zip"
+		File rnaseq_zip = "${bamname}_rnaseq_qualimap.zip"
         File bamqc_zip = "${bamname}_bamqc_qualimap.zip"
 	}
 }