Merge branch 'make_it_production_ready' into 'master'
QuaC - First major review See merge request center-for-computational-genomics-and-data-science/sciops/pipelines/quac!1
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- .gitmodules 6 additions, 0 deletions.gitmodules
- CONTRIBUTING.md 22 additions, 0 deletionsCONTRIBUTING.md
- Changelog.md 19 additions, 0 deletionsChangelog.md
- README.md 195 additions, 12 deletionsREADME.md
- configs/cluster_config.json 16 additions, 0 deletionsconfigs/cluster_config.json
- configs/env/multiqc.yaml 7 additions, 0 deletionsconfigs/env/multiqc.yaml
- configs/env/quac.yaml 15 additions, 0 deletionsconfigs/env/quac.yaml
- configs/snakemake_slurm_profile 1 addition, 0 deletionsconfigs/snakemake_slurm_profile
- configs/workflow.yaml 2 additions, 5 deletionsconfigs/workflow.yaml
- src/create_dummy_ped.py 41 additions, 54 deletionssrc/create_dummy_ped.py
- src/run_pipeline.sh 0 additions, 14 deletionssrc/run_pipeline.sh
- src/run_quac.py 233 additions, 0 deletionssrc/run_quac.py
- src/utility_cgds 1 addition, 0 deletionssrc/utility_cgds
- workflow/Snakefile 15 additions, 13 deletionsworkflow/Snakefile
- workflow/rules/aggregate_results.smk 23 additions, 0 deletionsworkflow/rules/aggregate_results.smk
- workflow/rules/common.smk 51 additions, 53 deletionsworkflow/rules/common.smk
- workflow/rules/coverage_analysis.smk 47 additions, 44 deletionsworkflow/rules/coverage_analysis.smk
- workflow/rules/relatedness_ancestry.smk 43 additions, 37 deletionsworkflow/rules/relatedness_ancestry.smk
- workflow/rules/within_species_contamintation.smk 20 additions, 15 deletionsworkflow/rules/within_species_contamintation.smk
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