fixed file path

UPHL-BioNGS · Aug 3, 2023 · d8c43ec · d8c43ec
1 parent d75b9f5
commit d8c43ec
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml
@@ -24,11 +24,11 @@ jobs:
         run: |
           docker --version
 
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz           && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
+          wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
+          wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
+          wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
+          wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/863/225/GCA_904863225.1_KSB1_6J/GCA_904863225.1_KSB1_6J_genomic.fna.gz           && gzip -d GCA_904863225.1_KSB1_6J_genomic.fna.gz
           
           mkdir fastas
           mv *fna fastas/.
@@ -37,7 +37,7 @@ jobs:
 
       - name: Check MSA files
         run: |
-          for file in grandeur/roary/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk snp_matrix_with_qc.txt
+          for file in grandeur/roary/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk grandeur/snp-dists/snp_matrix_with_qc.txt
           do
             head $file
             wc -l $file