Concat reads for mitohifi input

sanger-tol · Oct 6, 2023 · 57beb02 · 57beb02
1 parent d4336a1
commit 57beb02
Showing 1 changed file with 4 additions and 3 deletions.
diff --git a/subworkflows/local/organelles.nf b/subworkflows/local/organelles.nf
@@ -1,10 +1,11 @@
 include { MITOHIFI_FINDMITOREFERENCE                    } from '../../modules/nf-core/mitohifi/findmitoreference/main'
 include { MITOHIFI_MITOHIFI as MITOHIFI_MITOHIFI_READS  } from '../../modules/nf-core/mitohifi/mitohifi/main'
 include { MITOHIFI_MITOHIFI as MITOHIFI_MITOHIFI_ASM    } from '../../modules/nf-core/mitohifi/mitohifi/main'
+include { CAT_CAT as CAT_CAT_MITOHIFI                   } from "../../modules/nf-core/cat/cat/main"
 
 workflow ORGANELLES {
     take:
-    hifi_reads  // channel: [ val(meta), datafile  ]
+    hifi_reads  // channel: [ val(meta), [datafile]  ]
     contigs     // channel: [ val(meta), datafile ] 
     mito_info   // channel: [ val(species), val(min_length), val(code), val(email) ]
 
@@ -17,9 +18,9 @@ workflow ORGANELLES {
     mito_info.map{ species, min_length, code, email -> email}.set{email}
     MITOHIFI_FINDMITOREFERENCE(species, email, min_length)
 
-    // TODO: concat reads
     if ( hifi_reads ) {
-        MITOHIFI_MITOHIFI_READS( hifi_reads.map{meta, hifi -> [meta, hifi, []]}, 
+        CAT_CAT_MITOHIFI(hifi_reads)
+        MITOHIFI_MITOHIFI_READS( CAT_CAT_MITOHIFI.out.file_out.map{meta, hifi -> [meta, hifi, []]}, 
                         MITOHIFI_FINDMITOREFERENCE.out.fasta,
                         MITOHIFI_FINDMITOREFERENCE.out.gb,
                         code)