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rename modules; seperate output paths and workflow paths
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- .gitignore 6 additions, 5 deletions.gitignore
- .gitmodules 6 additions, 6 deletions.gitmodules
- README.md 15 additions, 15 deletionsREADME.md
- Snakefile 26 additions, 31 deletionsSnakefile
- gitmodules/gatb-minia-pipeline 0 additions, 0 deletionsgitmodules/gatb-minia-pipeline
- gitmodules/popins4snake 0 additions, 0 deletionsgitmodules/popins4snake
- gitmodules/sickle 0 additions, 0 deletionsgitmodules/sickle
- snake_config.yaml 18 additions, 11 deletionssnake_config.yaml
- snakemodules/analysis.smk 10 additions, 10 deletionssnakemodules/analysis.smk
- snakemodules/analysis_develop.smk 225 additions, 0 deletionssnakemodules/analysis_develop.smk
- snakemodules/contigmap.smk 0 additions, 0 deletionssnakemodules/contigmap.smk
- snakemodules/crop_remapped.smk 0 additions, 0 deletionssnakemodules/crop_remapped.smk
- snakemodules/crop_unmapped.smk 0 additions, 0 deletionssnakemodules/crop_unmapped.smk
- snakemodules/download_krakendb.smk 0 additions, 0 deletionssnakemodules/download_krakendb.smk
- snakemodules/envs/bcftools.yml 0 additions, 0 deletionssnakemodules/envs/bcftools.yml
- snakemodules/envs/biopython.yml 0 additions, 0 deletionssnakemodules/envs/biopython.yml
- snakemodules/envs/bwa.yml 0 additions, 0 deletionssnakemodules/envs/bwa.yml
- snakemodules/envs/kraken2.yml 0 additions, 0 deletionssnakemodules/envs/kraken2.yml
- snakemodules/envs/notebooks.yml 0 additions, 0 deletionssnakemodules/envs/notebooks.yml
- snakemodules/envs/py27.yml 0 additions, 0 deletionssnakemodules/envs/py27.yml
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