Update README.md #36
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| name: CI | |
| on: [push] | |
| jobs: | |
| test-snakemake-pipeline: | |
| name: Test Snakemake Pipeline | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8.13 | |
| - name: Add conda to system path | |
| run: | | |
| # $CONDA is an environment variable pointing to the root of the miniconda directory | |
| echo $CONDA/bin >> $GITHUB_PATH | |
| - name: Install dependencies | |
| run: | | |
| conda install mamba -c conda-forge | |
| - name: Set up environment | |
| run: | | |
| mamba create -n cinful | |
| mamba env update -n cinful --file cinful/env/cinful_conda.yml | |
| - name: align_with_verifiedCvab | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/blast_v_hmmer.with_verified.aln -F -j1 --keep-target-files --allowed-rules align_with_verifiedCvab -d .tests/align_with_verifiedCvab | |
| - name: bestHitsContigs | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/03_best_hits/best_hit_contigs.csv -F -j1 --keep-target-files --allowed-rules bestHitsContigs -d .tests/bestHitsContigs | |
| - name: best_Cvab_fasta | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/blast_v_hmmer.fa -F -j1 --keep-target-files --allowed-rules best_Cvab_fasta -d .tests/best_Cvab_fasta | |
| - name: best_Cvab_headers | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/blast_v_hmmer.headers -F -j1 --keep-target-files --allowed-rules best_Cvab_headers -d .tests/best_Cvab_headers | |
| - name: best_hits | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/03_best_hits/best_hits.csv -F -j1 --keep-target-files --allowed-rules best_hits -d .tests/best_hits | |
| - name: blast_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/blast.txt -F -j1 --keep-target-files --allowed-rules blast_CvaB -d .tests/blast_CvaB | |
| - name: blast_immunity_protein | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/immunity_proteins/blast.txt -F -j1 --keep-target-files --allowed-rules blast_immunity_protein -d .tests/blast_immunity_protein | |
| - name: blast_microcin | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/microcins/blast.txt -F -j1 --keep-target-files --allowed-rules blast_microcin -d .tests/blast_microcin | |
| - name: blast_v_hmmer_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/blast_v_hmmer.csv -F -j1 --keep-target-files --allowed-rules blast_v_hmmer_CvaB -d .tests/blast_v_hmmer_CvaB | |
| - name: blast_v_hmmer_immunity_protein | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/immunity_proteins/blast_v_hmmer.csv -F -j1 --keep-target-files --allowed-rules blast_v_hmmer_immunity_protein -d .tests/blast_v_hmmer_immunity_protein | |
| - name: blast_v_hmmer_microcin | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/microcins/blast_v_hmmer.csv -F -j1 --keep-target-files --allowed-rules blast_v_hmmer_microcin -d .tests/blast_v_hmmer_microcin | |
| - name: buildhmm_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/CvaB.verified.hmm -F -j1 --keep-target-files --allowed-rules buildhmm_CvaB -d .tests/buildhmm_CvaB | |
| - name: buildhmm_immunity_protein | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/immunity_proteins.verified.hmm -F -j1 --keep-target-files --allowed-rules buildhmm_immunity_protein -d .tests/buildhmm_immunity_protein | |
| - name: buildhmm_microcin | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/microcins.verified.hmm -F -j1 --keep-target-files --allowed-rules buildhmm_microcin -d .tests/buildhmm_microcin | |
| - name: candidate_immunity | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/03_best_hits/best_immunity_protein_candidates.csv -F -j1 --keep-target-files --allowed-rules candidate_immunity -d .tests/candidate_immunity | |
| - name: filter_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/filtered_nr.fa -F -j1 --keep-target-files --allowed-rules filter_CvaB -d .tests/filter_CvaB | |
| - name: filter_CvaB_hits | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/CvaB/preQC.csv cinful_out/01_orf_homology/CvaB/QC.csv -F -j1 --keep-target-files --allowed-rules filter_CvaB_hits -d .tests/filter_CvaB_hits | |
| - name: filter_immunity_protein | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/immunity_proteins/filtered_nr.fa -F -j1 --keep-target-files --allowed-rules filter_immunity_protein -d .tests/filter_immunity_protein | |
| - name: makeblastdb_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/CvaB.verified.pep.dmnd -F -j1 --keep-target-files --allowed-rules makeblastdb_CvaB -d .tests/makeblastdb_CvaB | |
| - name: makeblastdb_immunity_protein | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/immunity_proteins.verified.pep.phr -F -j1 --keep-target-files --allowed-rules makeblastdb_immunity_protein -d .tests/makeblastdb_immunity_protein | |
| - name: makeblastdb_microcin | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/microcins.verified.pep.phr -F -j1 --keep-target-files --allowed-rules makeblastdb_microcin -d .tests/makeblastdb_microcin | |
| - name: msa_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/CvaB.verified.aln -F -j1 --keep-target-files --allowed-rules msa_CvaB -d .tests/msa_CvaB | |
| - name: msa_immunity_protein | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/immunity_proteins.verified.aln -F -j1 --keep-target-files --allowed-rules msa_immunity_protein -d .tests/msa_immunity_protein | |
| - name: msa_microcin | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/microcins.verified.aln -F -j1 --keep-target-files --allowed-rules msa_microcin -d .tests/msa_microcin | |
| - name: prodigal | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/prodigal_out/colicinV_Ecoli_Shortened_test.faa -F -j1 --keep-target-files --allowed-rules prodigal -d .tests/prodigal | |
| - name: nonredundant_prodigal | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/prodigal_out.all.nr.faa cinful_out/01_orf_homology/prodigal_out.all.nr_expanded.csv -F -j1 --keep-target-files --allowed-rules nonredundant_prodigal -d .tests/nonredundant_prodigal | |
| - name: signalSeqHMM | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/01_orf_homology/microcins/signalSeq.hit.csv -F -j1 --keep-target-files --allowed-rules signalSeqHMM -d .tests/signalSeqHMM | |
| - name: write_CvaB | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/CvaB.verified.pep -F -j1 --keep-target-files --allowed-rules write_CvaB -d .tests/write_CvaB | |
| - name: write_immunity_proteins | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/immunity_proteins.verified.pep -F -j1 --keep-target-files --allowed-rules write_immunity_proteins -d .tests/write_immunity_proteins | |
| - name: write_microcins | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/00_dbs/microcins.verified.pep -F -j1 --keep-target-files --allowed-rules write_microcins -d .tests/write_microcins | |
| - name: merged_results | |
| run: | | |
| source activate cinful | |
| cd cinful | |
| python -m snakemake cinful_out/02_homology_results/all_merged.csv -F -j1 --keep-target-files --allowed-rules merged_results -d .tests/merged_results |