Uncommenting subworkflows to test and correcting multiple downloads f…

…rom artifacts
sanger-tol · Jan 15, 2025 · 19b356d · 19b356d
1 parent 5124b2a
commit 19b356d
Showing 1 changed file with 16 additions and 16 deletions.
diff --git a/workflows/ascc_organellar.nf b/workflows/ascc_organellar.nf
@@ -278,23 +278,23 @@ workflow ASCC_ORGANELLAR {
     // }
 
 
-    // SUBWORKFLOW: DIAMOND BLAST FOR INPUT ASSEMBLY
-    //
-    //qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames sskingdoms sphylums salltitles
-    if ( include_workflow_steps.contains('uniprot_diamond') && valid_length_fasta.valid || include_workflow_steps.contains('ALL') && valid_length_fasta.valid ) {
-        UP_DIAMOND (
-            valid_length_fasta.valid,
-            params.diamond_uniprot_database_path
-        )
-        un_full             = UP_DIAMOND.out.reformed.map{it[1]}
-        un_hits             = UP_DIAMOND.out.hits_file.map{it[1]}
-        ch_versions         = ch_versions.mix(UP_DIAMOND.out.versions)
-    } else {
-        un_hits             = []
-        un_full             = []
-    }
+    // // SUBWORKFLOW: DIAMOND BLAST FOR INPUT ASSEMBLY
+    // //
+    // //qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore staxids sscinames sskingdoms sphylums salltitles
+    // if ( include_workflow_steps.contains('uniprot_diamond') && valid_length_fasta.valid || include_workflow_steps.contains('ALL') && valid_length_fasta.valid ) {
+    //     UP_DIAMOND (
+    //         valid_length_fasta.valid,
+    //         params.diamond_uniprot_database_path
+    //     )
+    //     un_full             = UP_DIAMOND.out.reformed.map{it[1]}
+    //     un_hits             = UP_DIAMOND.out.hits_file.map{it[1]}
+    //     ch_versions         = ch_versions.mix(UP_DIAMOND.out.versions)
+    // } else {
+    //     un_hits             = []
+    //     un_full             = []
+    // }
 
-    ch_dot_genome           = ESSENTIAL_JOBS.out.dot_genome.map{it[1]}
+    // ch_dot_genome           = ESSENTIAL_JOBS.out.dot_genome.map{it[1]}
 
     // CREATE_BTK_DATASET (
     //     ESSENTIAL_JOBS.out.reference_tuple_from_GG,