From 585053013e1f1510008fe0817e42b2917373d83b Mon Sep 17 00:00:00 2001
From: TernovojD <ternovojd@hpc-node03.rki.local>
Date: Thu, 20 Jun 2024 10:53:54 +0200
Subject: [PATCH] bugfix: exiting the workflow

---
 eval.nf | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/eval.nf b/eval.nf
index 108d7da..99f30d7 100644
--- a/eval.nf
+++ b/eval.nf
@@ -5,12 +5,16 @@ GroovyObject help = (GroovyObject) HelppagesClass.newInstance();
 
 if (params.help) { exit 0, help.helpEval(workflow.manifest.version, params) }
 
+
+if (params.callsets_dir == "" && params.sample_sheet == "" || params.callsets_dir != "" && params.sample_sheet != ""){
+    exit 1, "Data input incorrect - please supply only one of the following parameters: sample_sheet, callsets_dir\n"
+}
+
 // include modules - here, modules are single processes
 include { SAMTOOLS_FAIDX } from './modules/samtools/faidx/main.nf'
 include { HAPPY } from './modules/happy/main.nf'
 include { SOMPY_SUMMARY } from './modules/misc/main.nf'
 
-
 workflow{
     // ------------------
     // | Input channels |
@@ -18,7 +22,7 @@ workflow{
     ch_ref      = Channel.value("$baseDir/" + params.reference)
     ch_ref_idx  = SAMTOOLS_FAIDX(ch_ref)
 
-    if (params.callsets_dir != "" && params.sample_sheet == "") {
+    if (params.callsets_dir != "") {
 
         ch_callsets = Channel.fromPath(params.callsets_dir + "/" + "*.{vcf,vcf.gz}", checkIfExists: true)
         ch_callsets
@@ -36,7 +40,7 @@ workflow{
             .set {ch_variantsets_map}
         // ch_variantsets_map.view()
 
-    } else if (params.sample_sheet != "" && params.callsets_dir == "") { 
+    } else { 
 
         ch_variantsets_map = Channel
             .fromPath(params.sample_sheet, checkIfExists: true)
@@ -44,10 +48,6 @@ workflow{
             .map {row -> [row["index"] as Integer, row["truthset"], row["callset"]]}
             // .view()
 
-    } else {
-
-        exit 1, "ERROR: Data input incorrect - please supply only one of the following parameters: sample_sheet, callsets_dir\n"
-
     }
 
     // ------------------