Skip input files which don't exist

FredHutch · Jan 30, 2024 · 4eea9f4 · 4eea9f4
1 parent 76a3453
commit 4eea9f4
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 0 deletions.
diff --git a/download_genes.nf b/download_genes.nf
@@ -46,11 +46,13 @@ workflow {
     // Parse the CSV path(s), if provided
     Channel
         .fromPath( params.genome_csv.split(',').toList() )
+        .filter { it.exists() }
         .set { gene_manifest_csv }
 
     // Parse the TSV path(s), if provided
     Channel
         .fromPath( params.genome_tsv.split(',').toList() )
+        .filter { it.exists() }
         .set { gene_manifest_tsv }
 
     // Download the genes for each genome

diff --git a/download_genomes.nf b/download_genomes.nf
@@ -46,11 +46,13 @@ workflow {
     // Parse the CSV path(s), if provided
     Channel
         .fromPath( params.genome_csv.split(',').toList() )
+        .filter { it.exists() }
         .set { genome_manifest_csv }
 
     // Parse the TSV path(s), if provided
     Channel
         .fromPath( params.genome_tsv.split(',').toList() )
+        .filter { it.exists() }
         .set { genome_manifest_tsv }
 
     // Download the genomes for each genome