Improve user experience if --reads is not provided

ctmrbio · May 7, 2021 · 4e64f42 · 4e64f42
1 parent 1741e36
commit 4e64f42
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/bactpipe.nf b/bactpipe.nf
@@ -52,6 +52,10 @@ if ( ! params.kraken2_db ) {
 	log.warn "No Kraken2 database specified. Use --kraken2_db /path/to/db to use Kraken2 to classify samples and determine gram stain."
 }
 
+if ( ! params.reads ) {
+    log.error "No reads specified. It is required to specify --reads 'path/to/*_{1,2}.fastq.gz' (note the single quotes)"
+    exit(1)
+}
 
 //================================================================================
 // Prepare channels