basic_functionality

AggressiveHayBale · Oct 4, 2022 · 5274bfc · 5274bfc
1 parent b2a7aeb
commit 5274bfc
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diff --git a/workflows/annotation_wf.nf b/workflows/annotation_wf.nf
@@ -7,14 +7,14 @@ include { prokka } from './workflows/subworkflows/prokka_wf.nf'
 
 workflow annotation_wf{
     take: 
-        csv_ch //val(name) path(to_fasta)
+        fasta_mod_ch // val(name), path(dir), path(contigsplit), path(noise)
 
     main: 
     //prokka
 
     //if (params.prokka_db) { prokka_db = file(params.prokka_db) }
     //    else { prokka_db = prokka_database() }
-    prokka(Path)
+    prokka(name, dir)
     //bakta
 
     //if (params.bakta_db) { bakta_db = file(params.bakta_db) }

diff --git a/workflows/fasta_mod_wf.nf b/workflows/fasta_mod_wf.nf
@@ -0,0 +1,18 @@
+process fasta_mod_wf {
+    label 'ubuntu'
+    input: 
+        tuple val(name), path(dir), val(contig), val(noise)
+
+    output: 
+        tuple val(name), path(dir), path("${name}_contigsplit.fasta"), path("${name}_noise.fasta"), emit: fasta_mod_ch
+    script: 
+    """
+        splitter.sh ${name} ${dir} ${contig}
+        noise.sh ${name} ${dir} ${noise}
+    """
+    stub:
+    """
+        touch "${name}"_contigsplit.fasta
+        touch "${name}"_noise.fasta
+    """
+