Merge pull request #186 from erikrikarddaniel/cat-prokka-ffn

Output concatenated ffn files from Prokka
nf-core · Sep 26, 2023 · 36157f5 · 36157f5
2 parents f81dce8 + be351ba
commit 36157f5
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -192,8 +192,8 @@ process {
         ]
     }
 
-    withName: 'FNA_CAT' {
-        ext.prefix = 'prokka.fna.gz'
+    withName: 'FFN_CAT' {
+        ext.prefix = 'prokka.ffn.gz'
         publishDir = [
             path: { "${params.outdir}/prokka" },
             mode: 'copy',

diff --git a/subworkflows/local/prokka_subsets.nf b/subworkflows/local/prokka_subsets.nf
@@ -5,7 +5,7 @@
 include { PROKKA               } from '../../modules/nf-core/prokka/main'
 include { CAT_CAT as GFF_CAT   } from '../../modules/nf-core/cat/cat/main'
 include { CAT_CAT as FAA_CAT   } from '../../modules/nf-core/cat/cat/main'
-include { CAT_CAT as FNA_CAT   } from '../../modules/nf-core/cat/cat/main'
+include { CAT_CAT as FFN_CAT   } from '../../modules/nf-core/cat/cat/main'
 include { PROKKAGFF2TSV        } from '../../modules/local/prokkagff2tsv'
 
 workflow PROKKA_SUBSETS {
@@ -32,18 +32,18 @@ workflow PROKKA_SUBSETS {
         ch_versions = ch_versions.mix(FAA_CAT.out.versions)
 
         contigs.map{ [ id:"${it[0].id}.prokka" ] }
-            .combine(PROKKA.out.fna.collect { it[1] }.map { [ it ] })
-            .set { ch_fna }
-        FNA_CAT ( ch_fna )
-        ch_versions = ch_versions.mix(FNA_CAT.out.versions)
+            .combine(PROKKA.out.ffn.collect { it[1] }.map { [ it ] })
+            .set { ch_ffn }
+        FFN_CAT ( ch_ffn )
+        ch_versions = ch_versions.mix(FFN_CAT.out.versions)
 
         PROKKAGFF2TSV ( GFF_CAT.out.file_out)
         ch_versions = ch_versions.mix(PROKKAGFF2TSV.out.versions)
 
     emit:
         gff        = GFF_CAT.out.file_out
         faa        = FAA_CAT.out.file_out
-        fna        = FNA_CAT.out.file_out
+        ffn        = FFN_CAT.out.file_out
         gfftsv     = PROKKAGFF2TSV.out.tsv
         prokka_log = ch_log
         versions   = ch_versions