Remove outdated amrplusplus scripts #156
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| name: Validate syntax and DAG | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| pull_request: [] # Do it on all PRs | |
| jobs: | |
| validate-syntax-and-dag: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| docker_tag: | |
| - 'stable' | |
| container: | |
| image: snakemake/snakemake:${{ matrix.docker_tag }} | |
| name: Validate syntax and DAG | |
| steps: | |
| - name: Check out code | |
| uses: actions/checkout@v3 | |
| - name: Create empty input files | |
| run: | | |
| ls | |
| mkdir -pv input | |
| touch input/test1_1.fq.gz input/test1_2.fq.gz | |
| touch input/test2_1.fq.gz input/test2_2.fq.gz | |
| - name: Create placeholder db files | |
| run: | | |
| ls | |
| mkdir -pv tmpdir | |
| mkdir -pv db/hg19 | |
| mkdir -pv db/metaphlan | |
| touch db/hg19/taxo.k2d | |
| touch db/metaphlan/test.1.bt2 | |
| - name: Modify config.yaml | |
| run: | | |
| ls | |
| sed -i 's/assess_depth: False/assess_depth: True/' config/config.yaml | |
| sed -i 's/sketch_compare: False/sketch_compare: True/' config/config.yaml | |
| sed -i 's/kaiju: False/kaiju: True/' config/config.yaml | |
| sed -i 's/kraken2: False/kraken2: True/' config/config.yaml | |
| sed -i 's/metaphlan: False/metaphlan: True/' config/config.yaml | |
| sed -i 's/humann: False/humann: True/' config/config.yaml | |
| sed -i 's/strainphlan: False/strainphlan: True/' config/config.yaml | |
| sed -i 's/groot: False/groot: True/' config/config.yaml | |
| sed -i 's/amrplusplus: False/amrplusplus: True/' config/config.yaml | |
| sed -i 's/assembly: False/assembly: True/' config/config.yaml | |
| sed -i 's/binning: False/binning: True/' config/config.yaml | |
| sed -i 's|db_path: \"\"|db_path: \"db/hg19\"|' config/config.yaml | |
| sed -i 's|db: \"\"|db: \"db\"|' config/config.yaml | |
| sed -i 's|bt2_db_dir: \"\"|bt2_db_dir: \"db/metaphlan\"|' config/config.yaml | |
| sed -i 's|bt2_index: \"\"|bt2_index: \"test\"|' config/config.yaml | |
| sed -i 's|_db: \"\"|_db: \"db\"|' config/config.yaml | |
| sed -i 's| index: \"\"| index: \"db\"|' config/config.yaml | |
| sed -i 's|kmer_distrib: \"\"|kmer_distrib: \"db\"|' config/config.yaml | |
| sed -i 's|tmpdir: \"/scratch\"|tmpdir: \"tmpdir\"|' config/config.yaml | |
| cat config/config.yaml | |
| - name: Run Snakemake | |
| run: | | |
| ls | |
| snakemake --dryrun | |