Change logic in samplesheet validation, ch_raw_short_reads should be …

…empty if no files are given
nf-core · Nov 29, 2024 · 67d44d0 · 67d44d0
1 parent 75a36f2
commit 67d44d0
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/subworkflows/local/utils_nfcore_mag_pipeline/main.nf b/subworkflows/local/utils_nfcore_mag_pipeline/main.nf
@@ -81,10 +81,10 @@ workflow PIPELINE_INITIALISATION {
         meta.run = meta.run == [] ? "0" : meta.run
         meta.single_end = params.single_end
 
-        if (params.single_end) {
+        if (params.single_end && sr1) {
             return [meta, [sr1]]
         }
-        else {
+        else if (sr1 && sr2) {
             return [meta, [sr1, sr2]]
         }
     }
@@ -323,7 +323,7 @@ def validateInputParameters(hybrid) {
 //
 def validateInputSamplesheet(meta, sr1, sr2, lr) {
 
-    if (!sr2 && !params.single_end) {
+    if ((!sr2 && !lr) && !params.single_end) {
         error("[nf-core/mag] ERROR: Single-end data must be executed with `--single_end`. Note that it is not possible to mix single- and paired-end data in one run! Check input TSV for sample: ${meta.id}")
     }
     if (sr2 && params.single_end) {