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Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
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Gregor Sturm 2020-07-16 16:48:47 +02:00 committed by GitHub
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@ -100,7 +100,9 @@ The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as descri
### Software requirements ### Software requirements
- Software requirements SHOULD be declared in a conda `environment.yml` file, including exact version numbers. Additionally, there MUST be a `Dockerfile` that containerizes the environment, or packages the software if conda is not available. - Software requirements SHOULD be declared in a conda `environment.yml` file, including exact version numbers. Additionally, there MUST be a `Dockerfile` that containerizes the environment, or packages the software if conda is not available.
- Docker containers MUST BE identified by their `sha256(Dockerfile + environment.yml)`. Like that, identical containers are implicitly re-used across subcommands. - Docker containers MUST BE identified by their `sha256(Dockerfile + environment.yml)`.
- Each module must have it's own `Dockerfile` and `environment.yml` file
- Care should be taken to maintain identical files for subcommands that use the same software. Then the hash tag will be the same and they will be implicitly re-used across subcommands.
### File formats ### File formats
- Wherever possible, [CRAM](https://en.wikipedia.org/wiki/CRAM_(file_format)) files SHOULD be used over BAM files. - Wherever possible, [CRAM](https://en.wikipedia.org/wiki/CRAM_(file_format)) files SHOULD be used over BAM files.