Merge pull request #565 from nf-core/warn-when-gtdb-filter-empty

Add warning GTDB-TK results will be empty if no contigs pass completeness filter

CHANGELOG.md

@@ -7,7 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [#548](https://github.com/nf-core/mag/pull/548) - Fixes to (reported by @maxibor, @PPpissar, @muniheart, @llborcard, fix by @maxibor)
+  - GTDBK-TK execution
+  - CAT/QUAST/DEPTH bin summary file name collisions
+  - BUSCO database parsing
+  - Correct CAT name files
 - [#562](https://github.com/nf-core/mag/pull/562) - Add CAT summary into the global bin_summary (by @maxibor)
+- [#565](https://github.com/nf-core/mag/pull/565) - Add warning of empty GTDB-TK results if no contigs pass completeness filter (fix by @jfy133 and @maxibor)
 
 ### `Changed`
 

subworkflows/local/gtdbtk.nf

@@ -77,6 +77,13 @@ workflow GTDBTK {
         error("Unsupported object given to --gtdb, database must be supplied as either a directory or a .tar.gz file!")
     }
 
+
+    // Print warning why GTDB-TK summary empty if passed channel gets no files
+    ch_filtered_bins.passed
+        .count()
+        .map{it == 0 ? log.warn("No contigs passed GTDB-TK min. completeness filters. GTDB-TK summary will execute but results will be empty!") : ""}
+
+
     GTDBTK_CLASSIFYWF (
         ch_filtered_bins.passed.groupTuple(),
         ch_db_for_gtdbtk,