refactor: Improve warning

beiko-lab · Sep 5, 2023 · 1ca7a13 · 1ca7a13
1 parent 4e8649e
commit 1ca7a13
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/subworkflows/local/assemblyqc.nf b/subworkflows/local/assemblyqc.nf
@@ -45,7 +45,7 @@ workflow CHECK_ASSEMBLIES {
         filtered_assemblies = assemblies
 
         if (params.apply_filtering) {
-            println 'WARNING: Your assemblies are being filtered \n(--apply_filtering is true)'
+            println '\033[0;33mWARN: Your assemblies are being filtered (--apply_filtering is true)'
 
             QUAST.out.transposed_report
                 .splitCsv(header: true, sep: '\t')
@@ -62,7 +62,7 @@ workflow CHECK_ASSEMBLIES {
         }
 
     emit:
-        filtered_assemblies
+        assemblies = filtered_assemblies
         quast_report = QUAST.out.transposed_report
         assemblyqc_software = ch_software_versions
         multiqc = ch_multiqc_files

diff --git a/workflows/arete.nf b/workflows/arete.nf
@@ -154,7 +154,7 @@ workflow ARETE {
     ch_software_versions = ch_software_versions.mix(CHECK_ASSEMBLIES.out.assemblyqc_software)
 
     if (params.apply_filtering) {
-        CHECK_ASSEMBLIES.out.filtered_assemblies
+        CHECK_ASSEMBLIES.out.assemblies
             .set { assemblies }
     }
 
@@ -380,7 +380,7 @@ workflow ANNOTATION {
         ch_multiqc_files = ch_multiqc_files.mix(CHECK_ASSEMBLIES.out.multiqc)
 
         if (params.apply_filtering) {
-            CHECK_ASSEMBLIES.out.filtered_assemblies
+            CHECK_ASSEMBLIES.out.assemblies
                 .set { assemblies }
         }
     }