first-commit

inputs

@@ -1,5 +1,5 @@
 {
-  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ project_name }}.samples_file": "{{ samples_file }}",
   "{{ 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",

tasks/bedtools.wdl

@@ -24,7 +24,6 @@ task multiqc {
 	}
 
 	output {
-		File multiqc_html = "multiqc_report.html"
-		Array[File] multiqc_txt = glob("multiqc_data/*")
+		File read_count = "revread_count.txt"
 	}
 }

workflow.wdl

@@ -2,11 +2,11 @@ import "./tasks/bedtools.wdl" as bedtools
 
 workflow {{ project_name }} {
 
-	File inputSamplesFile
+	File samples_file
 	File bed_file
-	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+	Array[Array[File]] samples_file = read_tsv(samples_file)
 
-	scatter (sample in inputSamples) {
+	scatter (sample in samples_file) {
 
 		call bedtools.bedtools as bedtools {
 			input: