added species-specific file check

UPHL-BioNGS · Apr 17, 2023 · 268e242 · 268e242
1 parent b8b0a67
commit 268e242
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Showing 3 changed files with 7 additions and 3 deletions.
diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
@@ -37,4 +37,6 @@ jobs:
           done
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
-          cat grandeur/grandeur_summary.tsv
+          cat grandeur/grandeur_summary.tsv
+          cat grandeur/shigatyper/shigatyper_results.txt
+          cat grandeur/serotypefinder/serotypefinder_results.txt
diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml
@@ -37,4 +37,5 @@ jobs:
           done
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
-          cat grandeur/grandeur_summary.tsv
+          cat grandeur/grandeur_summary.tsv
+          cat grandeur/seqsero2/seqsero2_results.txt
diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml
@@ -37,4 +37,5 @@ jobs:
           done
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
-          cat grandeur/grandeur_summary.tsv
+          cat grandeur/grandeur_summary.tsv
+          grep -i vibrio grandeur/fastani/fastani_summary.csv