refactor: add config to pivot modules

nf-core · Dec 6, 2024 · 32b34a1 · 32b34a1
1 parent e093df4
commit 32b34a1
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -468,9 +468,11 @@ process {
         ]
     }
 
-    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:CSVTK_JOIN' {
-        ext.args = "--fields 'UID,Read,miRNA,Variant,iso_5p,iso_3p,iso_add3p,iso_snp,iso_5p_nt,iso_3p_nt,iso_add3p_nt,iso_snp_nt' --tabs --outer-join --na \"0\" --out-delimiter \"\t\""
-        ext.prefix = "joined_samples_mirtop"
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:PIVOT_LONGER' {
+        publishDir = [ enabled: false ]
+    }
+
+    withName: 'NFCORE_SMRNASEQ:MIRNA_QUANT:PIVOT_WIDER' {
         publishDir = [
             path: { "${params.outdir}/mirna_quant/mirtop" },
             mode: params.publish_dir_mode,