Channel updates and bug fix for #178

sanger-tol · Nov 23, 2023 · febaeba · febaeba
1 parent dcf727e
commit febaeba
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Showing 2 changed files with 8 additions and 9 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -307,6 +307,13 @@ process {
         ext.args        = { "-k2,2 -nr -S${task.memory.mega - 100}M -T ." }
     }
 
+    //
+    // KMER
+    //
+    withName: CAT_CAT {
+        ext.prefix      = { "${meta.id}_merged.fasta.gz" }
+    }
+
     withName: FASTK_FASTK {
         ext.args        = "-k31 -t -P."
     }

diff --git a/subworkflows/local/kmer.nf b/subworkflows/local/kmer.nf
@@ -47,17 +47,9 @@ workflow KMER {
     ch_versions             = ch_versions.mix( CAT_CAT.out.versions.first() )
 
     //
-    // LOGIC: PRODUCE MERGED READS
-    //
-    CAT_CAT.out.file_out
-        .map{ meta, reads ->
-            reads.getName().endsWith('gz') ? [meta, reads.getParent().toString() + '/' + reads.getBaseName().toString() + '.fa.gz'] : [meta, reads.getParent().toString() + '/' + reads.getBaseName().toString() + '.fa']
-        }
-        .set{ ch_reads_merged }
-
     // MODULE: COUNT KMERS
     //
-    FASTK_FASTK( ch_reads_merged )
+    FASTK_FASTK( CAT_CAT.out.file_out )
     ch_versions             = ch_versions.mix( FASTK_FASTK.out.versions.first() )
 
     //