From 268e2426a1043f2a143af55efd814bfbdef17b8a Mon Sep 17 00:00:00 2001 From: Erin Young Date: Mon, 17 Apr 2023 15:01:21 -0600 Subject: [PATCH] added species-specific file check --- .github/workflows/ecoli.yml | 4 +++- .github/workflows/salmonella.yml | 3 ++- .github/workflows/vibrio.yml | 3 ++- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml index ab25b2f..b610388 100644 --- 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 \ No newline at end of file + cat grandeur/grandeur_summary.tsv + cat grandeur/shigatyper/shigatyper_results.txt + cat grandeur/serotypefinder/serotypefinder_results.txt \ No newline at end of file diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml index 4f6eebf..2b93058 100644 --- 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 \ No newline at end of file + cat grandeur/grandeur_summary.tsv + cat grandeur/seqsero2/seqsero2_results.txt \ No newline at end of file diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml index be28c16..7194679 100644 --- 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 \ No newline at end of file + cat grandeur/grandeur_summary.tsv + grep -i vibrio grandeur/fastani/fastani_summary.csv \ No newline at end of file