Merge pull request #40 from genomic-medicine-sweden/nanopore_docker

Update dockerfile for nanopore

Author: sofstam

.github/workflows/build_dockerfile.yml

@@ -1,11 +1,11 @@
-name: Update docker for artic-ncov2019-illumina
+name: Update docker for artic-ncov2019-illumina, artic-ncov2019-nanopore
 
 on:
  schedule:
    - cron: '0 0 * * *'
  push:
    branches:
-   - GHactions_37d2b7a
+   - nanopore_docker
 jobs:
   get-version:
     runs-on: ubuntu-latest
@@ -87,7 +87,12 @@ jobs:
          constellations_VER=$(cat versions/constellations-latest-version.txt | sed 's|v||')
          pangodesign_VER=$(cat versions/pangodesignation-latest-version.txt | sed 's|v||' )  
          docker build --no-cache -f environments/illumina/Dockerfile -t genomicmedicinesweden/gms-artic-illumina:latest -t genomicmedicinesweden/gms-artic-illumina:${{ steps.date.outputs.date }}-p-${REPO_VER}-L-${pangoLEARN_VER}-c-${constellations_VER}-d-${pangodesign_VER}-s-${scorpio_VER} .           
-     
+         #Build docker for nanopore
+         docker build --no-cache -f environments/nanopore/Dockerfile -t genomicmedicinesweden/gms-artic-nanopore:latest -t genomicmedicinesweden/gms-artic-nanopore:${{ steps.date.outputs.date }}-p-${REPO_VER}-L-${pangoLEARN_VER}-c-${constellations_VER}-d-${pangodesign_VER}-s-${scorpio_VER} .
+         #Build docker for pangolin-check for specific requirements
+         docker build --no-cache -f environments/nanopore/pangolin/Dockerfile -t genomicmedicinesweden/gms-artic-pangolin:latest -t genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-L-${pangoLEARN_VER}-c-${constellations_VER}-d-${pangodesign_VER}-s-${scorpio_VER} .
+
+
      - name: Push Docker image to DockerHub
        shell: bash
        run: |
@@ -98,4 +103,9 @@ jobs:
          pangodesign_VER=$(cat versions/pangodesignation-latest-version.txt | sed 's|v||' )
          docker image push genomicmedicinesweden/gms-artic-illumina:latest
          docker image push genomicmedicinesweden/gms-artic-illumina:${{ steps.date.outputs.date }}-p-${REPO_VER}-L-${pangoLEARN_VER}-c-${constellations_VER}-d-${pangodesign_VER}-s-${scorpio_VER}
-             
+         #Push to dockerhub for nanopore
+         docker image push genomicmedicinesweden/gms-artic-nanopore:latest
+         docker image push genomicmedicinesweden/gms-artic-nanopore:${{ steps.date.outputs.date }}-p-${REPO_VER}-L-${pangoLEARN_VER}-c-${constellations_VER}-d-${pangodesign_VER}-s-${scorpio_VER}   
+         #Push to dockerhub for pangolin with specific requirements
+         docker image push genomicmedicinesweden/gms-artic-pangolin:latest
+         docker image push genomicmedicinesweden/gms-artic-pangolin:${{ steps.date.outputs.date }}-p-${REPO_VER}-L-${pangoLEARN_VER}-c-${constellations_VER}-d-${pangodesign_VER}-s-${scorpio_VER}