revised

tasks/cuffdiff2.wdl

     File gtf
     File genome_directory
     String idx_prefix
-    String base = sub(basename(read),"\\.\\S+$", "")
+    String baseout
     String docker
 
     command {
-      cuffdiff ${gtf} -p 24 -o ${base} --no-diff -u -L ${base},${base}_rep -b ${genome_directory}/${idx_prefix}.fa ${bam} ${bam} 
+      cuffdiff ${gtf} -p 24 -o ${baseout} --no-diff -u -L ${base},${base}_rep -b ${genome_directory}/${idx_prefix}.fa ${bam} ${bam} 
     }
 
     runtime {

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