......

inputs

@@ -1,8 +1,8 @@
 {
     "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-    "{{ project_name }}.sample_id": "{{ sample_id }}",
-    "{{ project_name }}.read1": "{{ read1 }}",
-    "{{ project_name }}.read2": "{{ read2 }}",
+    #"{{ project_name }}.sample_id": "{{ sample_id }}",
+    #"{{ project_name }}.read1": "{{ read1 }}",
+    #"{{ project_name }}.read2": "{{ read2 }}",
     "{{ project_name }}.idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
     "{{ project_name }}.gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
     "{{ project_name }}.idx_prefix": "genome_snp_tran",
@@ -14,8 +14,8 @@
     "{{ project_name }}.stringtie.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
     "{{ project_name }}.fastp.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",
     "{{ project_name }}.fastp.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
-    "{{ project_name }}.adapter_sequence": "{{ adapter_sequence  }}",
-    "{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
+    #"{{ project_name }}.adapter_sequence": "{{ adapter_sequence  }}",
+    #"{{ project_name }}.adapter_sequence_r2": "{{ adapter_sequence_r2 }}",
     "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
     "{{ project_name }}.fastqc.disk_size": "150",
     "{{ project_name }}.gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
@@ -24,15 +24,15 @@
     "{{ project_name }}.qualimapBAMqc.disk_size": "500",
     "{{ project_name }}.fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
     "{{ project_name }}.fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
-    "{{ project_name }}.qualimapRNAseq.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+    #"{{ project_name }}.qualimapRNAseq.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
     "{{ project_name }}.screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
     "{{ project_name }}.fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
     "{{ project_name }}.multiqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
     "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
-    "{{ project_name }}.qualimapRNAseq.disk_size": "500",
+    #"{{ project_name }}.qualimapRNAseq.disk_size": "500",
     "{{ project_name }}.qualimapBAMqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
     "{{ project_name }}.qualimapBAMqc.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
-    "{{ project_name }}.qualimapRNAseq.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+    #"{{ project_name }}.qualimapRNAseq.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
     "{{ project_name }}.fastqscreen.disk_size": "100",
     "{{ project_name }}.multiqc.disk_size": "100",
     "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"

workflow.wdl

@@ -2,7 +2,6 @@ import "./tasks/fastp.wdl" as fastp
 import "./tasks/hisat2.wdl" as hisat2
 import "./tasks/samtools.wdl" as samtools
 import "./tasks/stringtie.wdl" as stringtie
-
 import "./tasks/fastqc.wdl" as fastqc
 import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc
@@ -13,20 +12,40 @@ workflow {{ project_name }} {
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 	
+	String fasta
+    	#String sample_id
+	#String adapter_sequence
+    	#String adapter_sequence_r2
+	String idx_prefix
+	String hisat2.docker
+	String samtools.docker
+	String stringtie.docker
+	String fastp.docker
+	String fastqscreen.docker
+	String multiqc.docker
+	String qualimapBAMqc.docker
+	String fastqc.docker
+	String hisat2.cluster
+	String samtools.cluster
+	String stringtie.cluster
+	String fastp.cluster
+	String fastqc.disk_size
+	String fastqscreen.cluster_config
+	String fastqc.cluster_config
+	String qualimapBAMqc.disk_size
+	String multiqc.cluster_config
+	String qualimapRNAseq.disk_size
+	String qualimapBAMqc.cluster_config
+	String qualimapRNAseq.cluster_config
+	String fastqscreen.disk_size
+	String multiqc.disk_size
 	File screen_ref_dir
 	File fastq_screen_conf
-	File read1
-	File read2
+	#File read1
+	#File read2
     	File idx
-
 	File gtf
-	String fasta
-    	String sample_id
-	
-	String adapter_sequence
-    	String adapter_sequence_r2
-	String idx_prefix
-    	File gtf
+	File ref_dir
 
 
 	scatter (quartet in inputSamples){