......

defaults

     "qualimapBAMqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
     "qualimapBAMqc_cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
     "qualimapBAMqc_disk_size": "500",
-    "qualimapRNAseqqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
-    "qualimapRNAseqqc_cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
-    "qualimapRNAseqqc_disk_size": "500",
+    "qualimapRNAseq_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+    "qualimapRNAseq_cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+    "qualimapRNAseq_disk_size": "500",
     "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
     "fastqscreen_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",

workflow.wdl

 import "./tasks/multiqc.wdl" as multiqc
 
 workflow {{ project_name }} {
-	
-	
-	
-	
-	
+	File inputSamplesFile
+	File idx
+	File screen_ref_dir
+	File fastq_screen_conf
+	File gtf
+	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
+	String fastp_docker
+	String adapter_sequence
+	String adapter_sequence_r2
+	String fastp_cluster
+	String umi_loc
+	String idx_prefix
+	String pen_intronlen
+	String fastqc_cluster_config
+	String fastqc_docker
+	String fastqscreen_docker
+	String fastqscreen_cluster_config
+	String hisat2_docker
+	String hisat2_cluster
+	String qualimapBAMqc_docker
+	String qualimapBAMqc_cluster_config
+	String qualimapRNAseq_docker
+	String qualimapRNAseq_cluster_config
+	String samtools_docker
+	String samtools_cluster
+	String stringtie_docker
+	String stringtie_cluster
+	String multiqc_cluster_config
+	String multiqc_docker
+	Int multiqc_disk_size
+	Int trim_front1 
+	Int trim_tail1 
+	Int max_len1 
+	Int trim_front2 
+	Int trim_tail2  
+	Int max_len2 
+	Int disable_adapter_trimming
+	Int length_required
+	Int umi_len
+	Int UMI
+	Int qualified_quality_phred
+	Int length_required1
+	Int disable_quality_filtering
+	Int pen_cansplice
+	Int pen_noncansplice
+	Int min_intronlen
+	Int max_intronlen
+	Int maxins
+	Int minins
+	Int fastqc_disk_size
+	Int fastqscreen_disk_size
+	Int qualimapBAMqc_disk_size
 	Int qualimapRNAseq_disk_size
+	Int insert_size
+	Int minimum_length_allowed_for_the_predicted_transcripts
+	Int Junctions_no_spliced_reads
+	Float minimum_isoform_abundance
+	Float maximum_fraction_of_muliplelocationmapped_reads
 }