Removed featureCounts and changed names of processes in Stringtie

IGDRion · Nov 26, 2024 · d683713 · d683713
1 parent ccb08e9
commit d683713
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Showing 5 changed files with 15 additions and 72 deletions.
diff --git a/modules/stringtie/stringtie_assemble.nf b/modules/stringtie/stringtie_assemble.nf
@@ -1,4 +1,4 @@
-process STRINGTIE_ASSEMBLE {
+process ASSEMBLE {
   conda (params.enable_conda ? "bioconda::stringtie" : null)
   container "${ workflow.containerEngine == 'Singularity' ? 
                 'https://depot.galaxyproject.org/singularity/stringtie%3A2.2.3--h43eeafb_0' :

diff --git a/modules/stringtie/stringtie_merge.nf b/modules/stringtie/stringtie_merge.nf
@@ -1,4 +1,4 @@
-process STRINGTIE_MERGE {
+process MERGE {
   conda (params.enable_conda ? "bioconda::stringtie" : null)
   container "${ workflow.containerEngine == 'Singularity' ? 
                 'https://depot.galaxyproject.org/singularity/stringtie%3A2.2.3--h43eeafb_0' :

diff --git a/modules/stringtie/stringtie_quant.nf b/modules/stringtie/stringtie_quant.nf
@@ -1,4 +1,4 @@
-process STRINGTIE_QUANTIFY {
+process QUANTIFY {
   conda (params.enable_conda ? "bioconda::stringtie" : null)
   container "${ workflow.containerEngine == 'Singularity' ? 
                 'https://depot.galaxyproject.org/singularity/stringtie%3A2.2.3--h43eeafb_0' :

diff --git a/modules/stringtie/stringtie_workflow.nf b/modules/stringtie/stringtie_workflow.nf
@@ -1,9 +1,8 @@
-include { STRINGTIE_ASSEMBLE             } from './stringtie_assemble.nf'
-include { STRINGTIE_MERGE                } from './stringtie_merge.nf'
-include { STRINGTIE_QUANTIFY             } from './stringtie_quant.nf'
+include { ASSEMBLE                       } from './stringtie_assemble.nf'
+include { MERGE                          } from './stringtie_merge.nf'
+include { QUANTIFY                       } from './stringtie_quant.nf'
 include { GFFCOMPARE                     } from '../gffcompare/gffcompare.nf'
 include { FORMAT_GFFCOMPARE              } from './stringtie_format_gffcompare.nf'
-include { SUBREAD_FEATURECOUNTS          } from '../subread/subread_featurecounts.nf'
 include { MERGE_COUNTS                   } from './stringtie_merge_counts.nf'
 
 workflow STRINGTIE {
@@ -13,30 +12,30 @@ workflow STRINGTIE {
     ref_fa
 
     main:
-    STRINGTIE_ASSEMBLE(
+    ASSEMBLE(
         samples, 
         input_gtf)
 
-    STRINGTIE_MERGE(
-        STRINGTIE_ASSEMBLE.out.stringtie_assemble_gtf.collect(), 
+    MERGE(
+        ASSEMBLE.out.stringtie_assemble_gtf.collect(), 
         input_gtf)
 
     GFFCOMPARE(
         input_gtf, 
         ref_fa, 
-        STRINGTIE_MERGE.out.stringtie_merged_gtf)
+        MERGE.out.stringtie_merged_gtf)
 
     FORMAT_GFFCOMPARE(
-        STRINGTIE_MERGE.out.stringtie_merged_gtf,
+        MERGE.out.stringtie_merged_gtf,
         GFFCOMPARE.out.tracking_file)
 
-    STRINGTIE_QUANTIFY(
+    QUANTIFY(
         samples,
-        STRINGTIE_MERGE.out.stringtie_merged_gtf)
+        MERGE.out.stringtie_merged_gtf)
 
     MERGE_COUNTS(
-        STRINGTIE_QUANTIFY.out.counts_gene.collect(), 
-        STRINGTIE_QUANTIFY.out.counts_transcript.collect())
+        QUANTIFY.out.counts_gene.collect(), 
+        QUANTIFY.out.counts_transcript.collect())
 
     emit:
     stringtie_gtf = FORMAT_GFFCOMPARE.out.stringtie_gtf

diff --git a/modules/subread/subread_featurecounts.nf b/modules/subread/subread_featurecounts.nf