Write normalized spectracounts #262
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| name: Continuous Integration | |
| on: | |
| push: | |
| branches: | |
| - development | |
| - master # master test only useful for badges | |
| pull_request: | |
| branches: | |
| - development | |
| - master # master test only useful for badges | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Build and push | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: . | |
| file: ./cicd/Dockerfile_CI | |
| tags: mosca:latest | |
| outputs: type=docker,dest=/tmp/mosca.tar | |
| - name: Create named volume | |
| run: docker volume create named_volume | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: mosca | |
| path: /tmp/mosca.tar | |
| preprocess: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: mosca | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/mosca.tar | |
| docker image ls -a | |
| - name: run preprocess | |
| run: | | |
| docker run mosca /bin/bash -c "rm -r MOSCARDO/output_rules/Preprocess; | |
| snakemake --cores all -R --until preprocess -s MOSCA/workflow/Snakefile --configfile MOSCARDO/configs/rules_config.json --use-conda" | |
| assembly: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: mosca | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/mosca.tar | |
| docker image ls -a | |
| - name: run assembly | |
| run: | | |
| docker run mosca /bin/bash -c "rm -r MOSCARDO/output_rules/Assembly; gunzip -r MOSCARDO/output_rules; | |
| touch MOSCARDO/output_rules/Preprocess/Trimmomatic/quality_trimmed_mg_forward_paired.fq; | |
| touch MOSCARDO/output_rules/Preprocess/Trimmomatic/quality_trimmed_mg_reverse_paired.fq; | |
| snakemake --cores all -R --until assembly -s MOSCA/workflow/Snakefile --configfile MOSCARDO/configs/rules_config.json --use-conda" | |
| binning: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| if: false # Blocked for now, since GHA don't provide enough memory to run this step ( 7Gb < 32Gb ) | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: mosca | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/mosca.tar | |
| docker image ls -a | |
| - name: run binning | |
| run: | | |
| docker run mosca /bin/bash -c "gunzip -r MOSCARDO/output_rules; | |
| touch MOSCARDO/output_rules/Preprocess/Trimmomatic/quality_trimmed_mg_forward_paired.fq; | |
| touch MOSCARDO/output_rules/Preprocess/Trimmomatic/quality_trimmed_mg_reverse_paired.fq; | |
| touch MOSCARDO/output_rules/Preprocess/sample_forward.fastq MOSCARDO/output_rules/Preprocess/sample_reverse.fastq; | |
| touch MOSCARDO/output_rules/Assembly/sample/contigs.fasta MOSCARDO/output_rules/Assembly/sample/scaffolds.fasta; | |
| snakemake --cores all -R --until binning -s MOSCA/workflow/Snakefile --configfile MOSCARDO/configs/rules_config.json --use-conda --ignore-incomplete" | |
| mgmt-workflow: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| if: false # Blocked for now, since GHA don't provide enough disk space to run this step | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: mosca | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/mosca.tar | |
| docker image ls -a | |
| - name: MGMT workflow | |
| run: docker run mosca /bin/bash -c "rm -r MOSCARDO/output_rules; mosca -c MOSCARDO/configs/mgmt_config.json" | |
| mgmp-workflow: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| if: false # Blocked for now, since GHA don't provide enough disk space to run this step | |
| steps: | |
| - name: Download artifact | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: mosca | |
| path: /tmp | |
| - name: Load Docker image | |
| run: | | |
| docker load --input /tmp/mosca.tar | |
| docker image ls -a | |
| - name: Create named volume | |
| run: docker volume create named_volume | |
| - name: MGMP workflow | |
| run: > | |
| docker run -v named_volume:/data -v /var/run/docker.sock:/var/run/docker.sock mosca /bin/bash | |
| -c "rm -r MOSCARDO/output_rules; gunzip -v MOSCARDO/input/*/mp*.RAW.gz; | |
| mosca -c MOSCARDO/configs/mgmp_config.json" |