revised-cufflinks

defaults

   "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",
-  "cuffdiff2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1"
-
+  "cufflinks_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1"
 }

tasks/cuffdiff2.wdl

-task cuffdiff2 {
-    File gtf
-    File genome_directory
-    String idx_prefix
-    String baseout
-    String docker
-
-    command {
-      cuffdiff ${gtf} -p 24 -o ${baseout} --no-diff -u -L ${base},${base}_rep -b ${genome_directory}/${idx_prefix}.fa ${bam} ${bam} 
-    }
-
-    runtime {
-      dockerTag: docker
-    }
-    
-    output {
-      File isoforms_count = "${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"
-    }
-}

tasks/cufflinks.wdl

+task cufflinks {
+    File gtf
+    File accepted_hits
+    File genome_directory
+    String idx_prefix
+    String baseout
+    String docker
+
+    command {
+      cufflinks ${gtf} -p 24 -o ${baseout} ${accepted_hits}
+
+    runtime {
+      dockerTag: docker
+    }
+    
+    output {
+      File isoforms_count = "${baseout}/isoforms.fpkm_tracking"
+      File genes_count = "${baseout}/genes.fpkm_tracking"
+      File skipped_gtf = "${baseout}/skipped.gtf"
+      File transcripts_gtf = "${baseout}/transcripts.gtf"
+    }
+}