From 4eea9f47cb957d59ff69b78290e60bfce243d434 Mon Sep 17 00:00:00 2001
From: Sam Minot <sminot@fredhutch.org>
Date: Tue, 30 Jan 2024 06:05:43 -0800
Subject: [PATCH] Skip input files which don't exist

---
 download_genes.nf   | 2 ++
 download_genomes.nf | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/download_genes.nf b/download_genes.nf
index 3d72ae4..bf8c3d5 100644
--- 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
index f90349c..92b0795 100644
--- 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