From 28d69a9120dfdf9c929b55287440218cd5ab8402 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Thu, 3 Aug 2023 13:00:39 -0600
Subject: [PATCH] specifies special files

---
 .github/workflows/ecoli.yml        | 11 +++++++++--
 .github/workflows/just_msa.yml     |  8 ++++++++
 .github/workflows/legionella.yml   |  9 ++++++++-
 .github/workflows/run_workflow.yml |  9 ++++++++-
 .github/workflows/salmonella.yml   | 11 ++++++++++-
 .github/workflows/strepA.yml       |  9 ++++++++-
 .github/workflows/strep_pneumo.yml | 10 +++++++++-
 .github/workflows/vibrio.yml       |  4 +++-
 8 files changed, 63 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
index b610388..f66c2f0 100644
--- a/.github/workflows/ecoli.yml
+++ b/.github/workflows/ecoli.yml
@@ -38,5 +38,12 @@ jobs:
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
           cat grandeur/grandeur_summary.tsv
-          cat grandeur/shigatyper/shigatyper_results.txt
-          cat grandeur/serotypefinder/serotypefinder_results.txt
\ No newline at end of file
+          
+      - name: Check E. coli file
+        run: |
+          for file in grandeur/shigatyper/shigatyper_results.txt grandeur/serotypefinder/serotypefinder_results.txt
+          do
+            head $file
+            wc -l $file
+          done
+  
\ No newline at end of file
diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml
index c0cb407..0a9a38b 100644
--- a/.github/workflows/just_msa.yml
+++ b/.github/workflows/just_msa.yml
@@ -34,3 +34,11 @@ jobs:
           mv *fna fastas/.
 
           nextflow run . -profile docker,just_msa --maxcpus 2 --medcpus 2
+
+      - name: Check MSA files
+        run: |
+          for file in grandeur/roary/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk snp_matrix_with_qc.txt
+          do
+            head $file
+            wc -l $file
+          done
diff --git a/.github/workflows/legionella.yml b/.github/workflows/legionella.yml
index 3a27757..5d28836 100644
--- a/.github/workflows/legionella.yml
+++ b/.github/workflows/legionella.yml
@@ -40,4 +40,11 @@ jobs:
           
           cat grandeur/grandeur_summary.tsv
 
-          cat grandeur/legsta/legsta_summary.csv
\ No newline at end of file
+      - name: Check Legionella file
+        run: |
+          for file in grandeur/legsta/legsta_summary.csv
+          do
+            head $file
+            wc -l $file
+          done
+  
\ No newline at end of file
diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
index ea607bb..6eeea18 100644
--- a/.github/workflows/run_workflow.yml
+++ b/.github/workflows/run_workflow.yml
@@ -31,4 +31,11 @@ jobs:
           mv *fastq.gz reads/.
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
           cat grandeur/grandeur_summary.tsv
-          
+      
+      - name: Check summary files
+        run: |
+          for file in grandeur/mlst/mlst_summary.tsv
+          do
+            head $file
+            wc -l $file
+          done
diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml
index 2b93058..73087ed 100644
--- a/.github/workflows/salmonella.yml
+++ b/.github/workflows/salmonella.yml
@@ -37,5 +37,14 @@ jobs:
           done
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
+
           cat grandeur/grandeur_summary.tsv
-          cat grandeur/seqsero2/seqsero2_results.txt
\ No newline at end of file
+
+      - name: Check Salmonella file
+        run: |
+          for file in grandeur/seqsero2/seqsero2_results.txt
+          do
+            head $file
+            wc -l $file
+          done
+  
\ No newline at end of file
diff --git a/.github/workflows/strepA.yml b/.github/workflows/strepA.yml
index 3ed8a18..5a4e1ed 100644
--- a/.github/workflows/strepA.yml
+++ b/.github/workflows/strepA.yml
@@ -38,4 +38,11 @@ jobs:
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
           cat grandeur/grandeur_summary.tsv
-          cat grandeur/emmtyper/emmtyper_summary.tsv
+
+      - name: Check Strep pneumo file
+        run: |
+          for file in grandeur/emmtyper/emmtyper_summary.tsv
+          do
+            head $file
+            wc -l $file
+          done
diff --git a/.github/workflows/strep_pneumo.yml b/.github/workflows/strep_pneumo.yml
index da2f3bf..4d4ff70 100644
--- a/.github/workflows/strep_pneumo.yml
+++ b/.github/workflows/strep_pneumo.yml
@@ -38,4 +38,12 @@ jobs:
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
           cat grandeur/grandeur_summary.tsv
-          cat grandeur/pbptyper/pbptyper_summary.tsv
\ No newline at end of file
+
+      - name: Check Strep pneumo file
+        run: |
+          for file in grandeur/pbptyper/pbptyper_summary.tsv
+          do
+            head $file
+            wc -l $file
+          done
+  
\ No newline at end of file
diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml
index 7194679..a160a90 100644
--- a/.github/workflows/vibrio.yml
+++ b/.github/workflows/vibrio.yml
@@ -38,4 +38,6 @@ jobs:
 
           nextflow run . -profile docker --maxcpus 2 --medcpus 2
           cat grandeur/grandeur_summary.tsv
-          grep -i vibrio grandeur/fastani/fastani_summary.csv
\ No newline at end of file
+
+      - name: Check Vibrio species
+        run: grep -i vibrio grandeur/fastani/fastani_summary.csv