revised-cufflinks

inputs

     "{{ project_name }}.read1": "{{ read1 }}",
     "{{ project_name }}.read2": "{{ read2 }}",
     "{{ project_name }}.gtf": "{{ gtf }}",
-    "{{ project_name }}.adapter": "{ adapter }",
+    "{{ project_name }}.adapter": "{{ adapter }}",
     "{{ project_name }}.genome_directory": "{{ genome_directory }}",
     "{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
     "{{ project_name }}.baseout": "{{ baseout }}",
     "{{ project_name }}.fastqc.docker": "{{ fastqc_docker }}",
     "{{ project_name }}.trimmomatic.docker": "{{ trimmomatic_docker }}",
     "{{ project_name }}.tophat2.docker": "{{ tophat2_docker }}",
-    "{{ project_name }}.cuffdiff2.docker": "{{ cuffdiff2_docker }}"
+    "{{ project_name }}.cufflinks_docker": "{{ cufflinks_docker }}"
 }

tasks/cufflinks.wdl

 task cufflinks {
     File gtf
+    File bam
     File accepted_hits
     File genome_directory
     String idx_prefix
     String docker
 
     command {
-      cufflinks ${gtf} -p 24 -o ${baseout} ${baseout}/accepted_hits.bam
+      cufflinks ${gtf} -p 24 -o ${baseout} ${bam}
 
     runtime {
       dockerTag: docker

workflow.wdl

 	}
 
 	call cufflinks.cufflinks as cufflinks {
-		input: gtf = gtf, genome_directory=genome_directory, idx_prefix=idx_prefix, baseout=baseout
+		input: gtf = gtf, bam = tophat2.accepted_hits, genome_directory=genome_directory, idx_prefix=idx_prefix, baseout=baseout
 	}
 }