Merge pull request #248 from silviamorins/master

Move process "convertGFFtoGTF" before "makeSTARindex"
nf-core · Jul 8, 2019 · e23da52 · e23da52
2 parents 839daa5 + 626796c
commit e23da52
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Showing 2 changed files with 22 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 ### Pipeline updates
 
+* Moved process "convertGFFtoGTF" before "makeSTARindex" [#215](https://github.com/nf-core/rnaseq/issues/215)
 * Add tximport and summarizedexperiment dependency [#171](https://github.com/nf-core/rnaseq/issues/171)
 * Appointed changes because of missing output of the multiqc_plots folder [#200](https://github.com/nf-core/rnaseq/issues/200)
 * Add Qualimap dependency [#202](https://github.com/nf-core/rnaseq/issues/202)

diff --git a/main.nf b/main.nf
@@ -339,6 +339,27 @@ process get_software_versions {
     """
 }
 
+/*
+ * PREPROCESSING - Convert GFF3 to GTF
+ */
+if(params.gff){
+  process convertGFFtoGTF {
+      tag "$gff"
+
+      input:
+      file gff from gffFile
+
+      output:
+      file "${gff.baseName}.gtf" into gtf_makeSTARindex, gtf_makeHisatSplicesites, gtf_makeHISATindex, gtf_makeBED12,
+            gtf_star, gtf_dupradar, gtf_featureCounts, gtf_stringtieFPKM
+
+      script:
+      """
+      gffread $gff -T -o ${gff.baseName}.gtf
+      """
+  }
+}
+
 /*
  * PREPROCESSING - Build STAR index
  */
@@ -434,26 +455,7 @@ if(params.aligner == 'hisat2' && !params.hisat2_index && params.fasta){
         """
     }
 }
-/*
- * PREPROCESSING - Convert GFF3 to GTF
- */
-if(params.gff){
-  process convertGFFtoGTF {
-      tag "$gff"
-
-      input:
-      file gff from gffFile
 
-      output:
-      file "${gff.baseName}.gtf" into gtf_makeSTARindex, gtf_makeHisatSplicesites, gtf_makeHISATindex, gtf_makeBED12,
-            gtf_star, gtf_dupradar, gtf_featureCounts, gtf_stringtieFPKM
-
-      script:
-      """
-      gffread $gff -T -o ${gff.baseName}.gtf
-      """
-  }
-}
 /*
  * PREPROCESSING - Build BED12 file
  */