Better find input files

FredHutch · Nov 14, 2023 · feb5d0d · feb5d0d
1 parent c27aa13
commit feb5d0d
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git a/deduplicate.nf b/deduplicate.nf
@@ -45,7 +45,7 @@ workflow {
 
     // Get all of the files in the specified folder
     Channel
-        .fromPath("${gene_folder}/*")
+        .fromPath("${gene_folder}/**")
         .ifEmpty { error "Cannot find any files at ${gene_folder}/*" }
         .set { gene_ch }
 

diff --git a/download_genes.nf b/download_genes.nf
@@ -37,8 +37,8 @@ workflow {
 
     // Parse the CSV and raise an error if the path is not valid
     Channel
-        .fromPath( params.genome_csv )
-        .ifEmpty { error "Cannot find any file at '${params.genome_csv}'" }
+        .fromPath( params.genome_csv.split(',').toList() )
+        .ifEmpty { error "Cannot find any file(s) at '${params.genome_csv}'" }
         .set { gene_manifest }
 
     // Download the genes for each genome

diff --git a/download_genomes.nf b/download_genomes.nf
@@ -37,8 +37,8 @@ workflow {
 
     // Parse the CSV and raise an error if the path is not valid
     Channel
-        .fromPath( params.genome_csv )
-        .ifEmpty { error "Cannot find any file at '${params.genome_csv}'" }
+        .fromPath( params.genome_csv.split(',').toList() )
+        .ifEmpty { error "Cannot find any file(s) at '${params.genome_csv}'" }
         .set { genome_manifest }
 
     // Download the genomes for each genome