readded missing module configs after rebase

nf-core · Jul 18, 2024 · 4265950 · 4265950
1 parent 3039a80
commit 4265950
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Showing 3 changed files with 15 additions and 1 deletion.
diff --git a/conf/modules.config b/conf/modules.config
@@ -629,6 +629,19 @@ process {
         ext.suffix = "_benchmarking.tidy.bed"
     }
 
+    withName: '.*:BENCHMARKING:SORT' {
+        ext.args = "-k 1,1 -k2,2n -k3,3n -u"
+        ext.suffix = "combined.bed"
+    }
+
+    withName: '.*:BENCHMARKING:BEDTOOLS_MERGE' {
+        ext.args = "-s -c 6 -o distinct"
+    }
+
+    withName: '.*:BENCHMARKING:BEDTOOLS_GENOMECOV' {
+        ext.args = "-dz"
+    }
+
     withName: COMBINE_TRANSCRIPTOME_GTFS {
         ext.args = "-k 1,1 -k4,4n -k5,5n"
         ext.suffix = "gtf"

diff --git a/subworkflows/local/benchmarking.nf b/subworkflows/local/benchmarking.nf
@@ -34,6 +34,7 @@ workflow BENCHMARKING {
                             benchmarking: meta.benchmarking], bed]}
         .groupTuple()
 
+    ch_all.view {"all: $it"}
 
     SORT(ch_all)
 

diff --git a/subworkflows/local/circrna_discovery.nf b/subworkflows/local/circrna_discovery.nf
@@ -158,7 +158,7 @@ workflow CIRCRNA_DISCOVERY {
 
 
     emit:
-    tool_bed  = ANNOTATION.out.merged_bed
+    circrna_bed12  = ANNOTATION.out.merged_bed
     fasta          = ADD_BACKSPLICE.out.output
     annotation_bed = ANNOTATION.out.bed
     annotation_gtf = ANNOTATION.out.gtf