fixing #8

nf-core · Nov 16, 2018 · 6f5b5ec · 6f5b5ec
1 parent 1d23373
commit 6f5b5ec
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/main.nf b/main.nf
@@ -256,15 +256,15 @@ if (!params.Q2imported){
     /*
     * Create a channel for input read files
     */
-    if(params.readPaths){
+    if(!params.reads){
         Channel
             .from(params.readPaths)
             .map { row -> [ row[0], [file(row[1][0]), file(row[1][1])]] }
             .ifEmpty { exit 1, "params.readPaths was empty - no input files supplied" }
             .into { ch_read_pairs; ch_read_pairs_fastqc }
     } else {
         Channel
-            .fromFilePairs( params.reads, size: 2 )
+            .fromFilePairs( params.reads + params.extension, size: 2 )
             .ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!" }
             .into { ch_read_pairs; ch_read_pairs_fastqc }
     }