ID mapping columns now must be properly inputted #106
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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: upimapi:latest | |
| outputs: type=docker,dest=/tmp/upimapi.tar | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp/upimapi.tar | |
| txt-file-comma-separated: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp | |
| - name: Load Docker image | |
| run: docker load --input /tmp/upimapi.tar | |
| - name: IDs inputted through TXT file (comma-separated) | |
| run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/cicd/ids.csv -cols 'Entry&KEGG&Interacts with&Taxonomic lineage (SUPERKINGDOM)&Taxonomic lineage (SPECIES)&Taxonomic lineage IDs (SUPERKINGDOM)&Taxonomic lineage IDs (SPECIES)'" | |
| txt-file-newline-separated: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp | |
| - name: Load Docker image | |
| run: docker load --input /tmp/upimapi.tar | |
| - name: Full IDs inputted through TXT file (newline-separated) | |
| run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/cicd/full_ids.txt" | |
| blast-file: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp | |
| - name: Load Docker image | |
| run: docker load --input /tmp/upimapi.tar | |
| - name: IDs inputted through BLAST file | |
| run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/cicd/ids.blast -rd resources_directory --blast" | |
| get-fasta-sequences: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp | |
| - name: Load Docker image | |
| run: docker load --input /tmp/upimapi.tar | |
| - name: Obtain FASTA sequences | |
| run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/cicd/ids.csv -rd resources_directory --fasta" | |
| basic-id-mapping: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp | |
| - name: Load Docker image | |
| run: docker load --input /tmp/upimapi.tar | |
| - name: Perform basic ID mapping | |
| run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/cicd/ids.csv -rd resources_directory --from-db 'UniProtKB AC/ID' --to-db 'EMBL/GenBank/DDBJ CDS'" | |
| full-workflow: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: upimapi | |
| path: /tmp | |
| - name: Load Docker image | |
| run: docker load --input /tmp/upimapi.tar | |
| - name: Full workflow, TaxIDs DB at Species level | |
| run: docker run upimapi /bin/bash -c "upimapi -i UPIMAPI/cicd/proteomes.fasta -rd resources_directory -db taxids --taxids 2203,2223,2209,2162,119484,35554,29543,863" |