revised-cufflinks

inputs

     "{{ project_name }}.fastqc.docker": "{{ fastqc_docker }}",
     "{{ project_name }}.trimmomatic.docker": "{{ trimmomatic_docker }}",
     "{{ project_name }}.tophat2.docker": "{{ tophat2_docker }}",
-    "{{ project_name }}.cufflinks_docker": "{{ cufflinks_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 baseout