revised

defaults

 {
-  "{{ project_name }}.gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
+  "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf",
+  "genome_directory":"oss://pgx-reference-data/reference/tophat2/"
+  "idx_prefix":"tophat2"
   "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",

inputs

 {
     "{{ project_name }}.read1": "{{ read1 }}",
     "{{ project_name }}.read2": "{{ read2 }}",
-    "{{ project_name }}.adapter": "{{ adapter }}",
     "{{ project_name }}.gtf": "{{ gtf }}",
     "{{ project_name }}.genome_directory": "{{ genome_directory }}",
     "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",

tasks/cuffdiff2.wdl

     File gtf
     File genome_directory
     String idx_prefix
-    String baseout
+    String base = sub(basename(read),"\\.\\S+$", "")
     String docker
 
     command {
-      cuffdiff ${gtf} -p 24 -o ${baseout} --no-diff -u -L ${baseout},${baseout}_rep -b ${genome_directory}/${idx_prefix}.fa ${bam} ${bam} 
+      cuffdiff ${gtf} -p 24 -o ${base} --no-diff -u -L ${base},${base}_rep -b ${genome_directory}/${idx_prefix}.fa ${bam} ${bam} 
     }
 
     runtime {
     }
     
     output {
-      File isoforms_count = "${baseout}/isoforms.count_tracking"
-      File genes_count = "${baseout}/genes.count_tracking"
-      File cds_count = "${baseout}/cds.count_tracking"
-      File isoforms_fpkm = "${baseout}/isoforms.fpkm_tracking"
-      File genes_fpkm = "${baseout}/genes.fpkm_tracking"
-      File cds_fpkm = "${baseout}/cds.fpkm_tracking"
+      File isoforms_count = "${base}/isoforms.count_tracking"
+      File genes_count = "${base}/genes.count_tracking"
+      File cds_count = "${base}/cds.count_tracking"
+      File isoforms_fpkm = "${base}/isoforms.fpkm_tracking"
+      File genes_fpkm = "${base}/genes.fpkm_tracking"
+      File cds_fpkm = "${base}/cds.fpkm_tracking"
     }
 }

tasks/tophat2.wdl

 task tophat2 {
    File gtf
    File genome_directory
+   String base = sub(basename(read),"\\.\\S+$", "")
    String idx_prefix
    File read_1P
    File read_2P
    String docker
 
    command {
-      tophat2 -p 24 -o ${baseout} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read_1P} ${read_2P}
+      tophat2 -p 24 -o ${base} -G ${gtf} --library-type fr-unstranded --solexa-quals ${genome_directory}/${idx_prefix} ${read_1P} ${read_2P}
    }
    
    runtime { 

tasks/trimmomatic.wdl

 	File read1
 	File read2
 	File adapter
-	String baseout
-	String baseout_gz = baseout + ".fq.gz"
+	String base = sub(basename(read),"\\.\\S+$", "")
 	String docker
 
 	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
+  	trimmomatic PE -threads 20 -phred33 ${read1} ${read2}  -baseout ${base}.fq.gz ILLUMINACLIP:${adapter}:2:30:10:1:true HEADCROP:10 LEADING:10 TRAILING:10 SLIDINGWINDOW:4:15 MINLEN:36
 	}
 
 	runtime {
 	}
 
 	output {
-		File read_1p = baseout + "_1P.fq.gz"
-		File read_2p = baseout + "_2P.fq.gz"
+		File read_1p = base + "_1P.fq.gz"
+		File read_2p = base + "_2P.fq.gz"
 	}
 }