Update build-and-deploy.yml (#41)

* Update build-and-deploy.yml

* lowercase m to get it to activate

* redo

Author: sage-wright

.github/workflows/build-and-deploy.yml

@@ -41,8 +41,8 @@ jobs:
         id: parse
         run: |
           echo "parsing ${{ matrix.added_modified }}"
-          tool=$(echo "${{ matrix.added_modified }}" | cut -f2 -d "/")
-          version=$(echo "${{ matrix.added_modified }}" | cut -f3 -d "/")
+          tool=$(echo "${{ matrix.added_modified }}" | cut -f1 -d "/")
+          version=$(echo "${{ matrix.added_modified }}" | cut -f2 -d "/")
           echo "found tool:version ${tool}:${version}"
           echo "tool=$tool" >> $GITHUB_OUTPUT
           echo "version=$version" >> $GITHUB_OUTPUT

irma/1.3.1-helper/Dockerfile

@@ -1,7 +1,7 @@
 # building from staphb/irma as the base
 FROM staphb/irma:1.3.1
 
-# Metadata
+# metadata
 LABEL base.image="staphb/irma:1.3.1"
 LABEL software="IRMA"
 LABEL software.version="1.3.1"

mlst/2.33.1/Dockerfile

@@ -16,7 +16,7 @@ LABEL maintainer.email="ines.mendes@theiagen.com"
 LABEL maintainer2="Curtis Kapsak"
 LABEL maintainer2.email="kapsakcj@gmail.com"
 
-# install dependencies via apt; cleanup apt garbage
+# Install dependencies via apt; cleanup apt garbage
 # deps needed specifically for db download scripts: libfile-which-perl, curl, parallel
 RUN apt-get update && apt-get install -y --no-install-recommends \
     wget \
@@ -95,4 +95,4 @@ RUN datasets download genome accession ${GENBANK_ACCESSION} --filename ${GENBANK
     mlst ${GENBANK_ACCESSION}-download/ncbi_dataset/data/${GENBANK_ACCESSION}/${GENBANK_ACCESSION}.genomic.fna | tee mlst.${GENBANK_ACCESSION}.tsv && \
     echo && \
     echo "Checking for ST15199 in the mlst results now..." && \
-    grep "15199" mlst.${GENBANK_ACCESSION}.tsv
+    grep "15199" mlst.${GENBANK_ACCESSION}.tsv