Add workflow checks that a study is provided otherwise pipeline could hang silently

Author: timrozday-mgnify

workflows/assemblysubmit.nf

@@ -151,6 +151,9 @@ workflow ASSEMBLYSUBMIT {
         'true' // skip_header - we want to keep the header from the first file and skip it for the rest
     )
 
+    if (!submission_study && !study_metadata) {
+        error("Either --submission_study or --study_metadata must be provided")
+    }
     def study_accession_ch
     if (submission_study) {
         // Use provided study accession directly

workflows/genomesubmit.nf

@@ -262,6 +262,9 @@ workflow GENOMESUBMIT {
     )
 
     // --------- Register study if accession not provided
+    if (!submission_study && !study_metadata) {
+        error("Either --submission_study or --study_metadata must be provided")
+    }
     def study_accession_ch
     if (submission_study) {
         study_accession_ch = channel.of(submission_study)

workflows/readsubmit.nf

@@ -69,6 +69,9 @@ workflow READSUBMIT {
             }
         }
 
+    if (!submission_study && !study_metadata) {
+        error("Either --submission_study or --study_metadata must be provided")
+    }
     def study_accession_ch
     if (submission_study) {
         // Use provided study accession directly