fixed variable typo

UPHL-BioNGS · Mar 2, 2023 · f2d0e83 · f2d0e83
1 parent 69408e5
commit f2d0e83
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 5 deletions.
diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
@@ -25,14 +25,13 @@ jobs:
           docker --version
           
           mkdir fastas 
-
-          for accesion in GCA_009738455.1_ASM973845v1 GCA_003019175.1_ASM301917v1 GCA_023823105.1_ASM2382310v1
+          for accession in GCA_009738455.1_ASM973845v1 GCA_003019175.1_ASM301917v1 GCA_023823105.1_ASM2382310v1
           do
             all=$(echo $accession | cut -f 2 -d "_")
             fir=$(echo $all | cut -c 1-3)
             mid=$(echo $all | cut -c 4-6)
             end=$(echo $all | cut -c 7-9)
-            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz
+            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/${fir}/${mid}/${end}/${accession}/${accession}_genomic.fna.gz
             gzip -d ${accession}_genomic.fna.gz
             mv ${accession}_genomic.fna fastas/.
           done

diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml
@@ -25,7 +25,7 @@ jobs:
           docker --version
           
           mkdir fastas
-          for accesion in GCA_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1
+          for accession in GCA_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1
           do
             all=$(echo $accession | cut -f 2 -d "_")
             fir=$(echo $all | cut -c 1-3)

diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml
@@ -25,7 +25,7 @@ jobs:
           docker --version
           
           mkdir fastas
-          for accesion in GCA_009665515.2_ASM966551v2 GCA_009763645.1_ASM976364v1 GCA_004355205.1_ASM435520v1 GCA_009665315.1_ASM966531v1 GCA_002953375.1_ASM295337v1
+          for accession in GCA_009665515.2_ASM966551v2 GCA_009763645.1_ASM976364v1 GCA_004355205.1_ASM435520v1 GCA_009665315.1_ASM966531v1 GCA_002953375.1_ASM295337v1
           do
             all=$(echo $accession | cut -f 2 -d "_")
             fir=$(echo $all | cut -c 1-3)