Added parameter for distributing quantification #73
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| name: CI | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build and push | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| file: ./Dockerfile | |
| tags: keggcharter:latest | |
| outputs: type=docker,dest=/tmp/keggcharter.tar | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: keggcharter | |
| path: /tmp/keggcharter.tar | |
| show-available-maps: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: keggcharter | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/keggcharter.tar | |
| docker image ls -a | |
| - name: Show available maps | |
| run: docker run keggcharter /bin/bash -c "keggcharter --show-available-maps" | |
| run-keggcharter: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: keggcharter | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/keggcharter.tar | |
| docker image ls -a | |
| - name: Run KEGGCharter | |
| run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -qcol MP1,MP2,MP3,MP4 -tc 'Taxonomic lineage (SPECIES)' -mm 00680" | |
| input-quantification-and-taxonomy: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: keggcharter | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/keggcharter.tar | |
| docker image ls -a | |
| - name: Run KEGGCharter with "input-quantification" and "input-taxonomy" parameters | |
| run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -iq -it 'My community' -mm 00680" | |
| include-missing-genomes: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: keggcharter | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/keggcharter.tar | |
| docker image ls -a | |
| - name: Run KEGGCharter with "include-missing-genomes" parameter | |
| run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -qcol MP1,MP2,MP3,MP4 -tc 'Taxonomic lineage (SPECIES)' -mm 00680 --include-missing-genomes" | |
| map-all: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: keggcharter | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/keggcharter.tar | |
| docker image ls -a | |
| - name: Run KEGGCharter with "map-all" parameter | |
| run: docker run keggcharter /bin/bash -c "keggcharter -f KEGGCharter/cicd/keggcharter_input.tsv -rd resources_directory -keggc 'KEGG' -koc 'KO' -ecc 'EC number' -cogc 'COG ID' -qcol MP1,MP2,MP3,MP4 -tc 'Taxonomic lineage (SPECIES)' -mm 00680 --map-all" |