fixed typos

.github/workflows/add_fastani_ref.yml

@@ -51,7 +51,6 @@ jobs:
 
         - name: Download fastani refs
           run: |
-              mkdir refs
               for accession in GCA_009665515.2_ASM966551v2 GCA_009763645.1_ASM976364v1
               do
                   all=$(echo $accession | cut -f 2 -d "_")

.github/workflows/legionella.yml

@@ -42,7 +42,7 @@ jobs:
 
       - name: Check Legionella file
         run: |
-          for file in grandeur/elgato/elgato_summary.csv
+          for file in grandeur/elgato/elgato_summary.tsv
           do
             head $file
             wc -l $file

.github/workflows/sample_sheet.yml

@@ -31,7 +31,7 @@ jobs:
           mv *fastq.gz reads/.
 
           echo "sample,fastq_1,fastq_2" > sample_sheet.csv
-          echo "SRR2838702,reads/SRR2838702_1.fastq.gz,reads/SRR2838702_2.fastq.gz"
+          echo "SRR2838702,reads/SRR2838702_1.fastq.gz,reads/SRR2838702_2.fastq.gz" >> sample_sheet.csv
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --sample_sheet sample_sheet.csv --skip_extras
           cat grandeur/grandeur_summary.tsv