add-cluster

defaults

@@ -6,5 +6,6 @@
   "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",
   "trimmomatic_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.3.8",
   "tophat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tophat2:2.0.14",
+  "tophat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
   "cufflinks_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1"
 }

inputs

@@ -9,5 +9,6 @@
     "{{ project_name }}.fastqc.docker": "{{ fastqc_docker }}",
     "{{ project_name }}.trimmomatic.docker": "{{ trimmomatic_docker }}",
     "{{ project_name }}.tophat2.docker": "{{ tophat2_docker }}",
+    "{{ project_name }}.tophat2.cluster": "{{ tophat2_cluster }}",
     "{{ project_name }}.cufflinks.docker": "{{ cufflinks_docker }}"
 }

tasks/cufflinks.wdl

@@ -5,6 +5,7 @@ task cufflinks {
     String idx_prefix
     String baseout
     String docker
+    String cluster
 
     command {
       cufflinks ${gtf} -p 24 -o ${baseout} ${bam}

tasks/fastqc.wdl

@@ -1,6 +1,7 @@
 task qc {
 	File read
 	String docker
+	String cluster
 	String out_dir = "./"
 
 	command {

tasks/tophat2.wdl

@@ -6,6 +6,7 @@ task tophat2 {
    File read_2P
    String baseout
    String docker
+   String cluster
 
    command {
       tophat2 -p 24 -o ${baseout} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read_1P} ${read_2P}

tasks/trimmomatic.wdl

@@ -5,6 +5,7 @@ task trimmomatic {
 	String baseout
 	String baseout_gz = baseout + ".fq.gz"
 	String docker
+	String cluster
 
 	command {
   	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${baseout_gz} ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36