specifies special files

.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
+          
+      - 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
+  

.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

.github/workflows/legionella.yml

@@ -40,4 +40,11 @@ jobs:
           
           cat grandeur/grandeur_summary.tsv
 
-          cat grandeur/legsta/legsta_summary.csv
+      - name: Check Legionella file
+        run: |
+          for file in grandeur/legsta/legsta_summary.csv
+          do
+            head $file
+            wc -l $file
+          done
+  

.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

.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
+
+      - name: Check Salmonella file
+        run: |
+          for file in grandeur/seqsero2/seqsero2_results.txt
+          do
+            head $file
+            wc -l $file
+          done
+  

.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

.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
+
+      - name: Check Strep pneumo file
+        run: |
+          for file in grandeur/pbptyper/pbptyper_summary.tsv
+          do
+            head $file
+            wc -l $file
+          done
+  

.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
+
+      - name: Check Vibrio species
+        run: grep -i vibrio grandeur/fastani/fastani_summary.csv