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```
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The workflow code goes into a subfolder `workflow`, while the configuration is stored in a subfolder `config`. Inside of the `workflow` subfolder, the central `Snakefile` marks the entrypoint of the workflow. Results are written into subfolder `results. Inside of the `results` subfolder, results are stored following the same structure than inside `workflow` subfolder.
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# Environment
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Softwares and dependencies can be run directly on the local system or using environments such as containers or using a package management system.
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## Containers
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[](https://singularity-hub.org/collections/2878)
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We provide ready to run versions of container built with [Singularity containers](https://www.sylabs.io/). All required softwares to run the workflow have been installed within this container. User can either download the ready-to-use built container OR build this container instead to download it using the [Singularity.obitools](Singularity.obitools) recipe. In both case, it gives an `obitools.simg` file. Absolute path to access to the container file fills the field `singularity:` into [config.yaml](config/)
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## Conda
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Softwares can be installed throught a conda environment. Each rule loads its own environment. Environment files are stored at `workflow/envs/obitools_envs.yaml`.
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# Wildcards
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Output and input can take any values. We defined them as wildcards. We use 4 wildcards:
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| ... | ... | @@ -231,3 +217,17 @@ demultiplex","projet", "marker","run", "plaque","sample","barcode5","barcode3"," |
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# Environment
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Softwares and dependencies can be run directly on the local system or using environments such as containers or using a package management system.
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## Containers
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[](https://singularity-hub.org/collections/2878)
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We provide ready to run versions of container built with [Singularity containers](https://www.sylabs.io/). All required softwares to run the workflow have been installed within this container. User can either download the ready-to-use built container OR build this container instead to download it using the [Singularity.obitools](Singularity.obitools) recipe. In both case, it gives an `obitools.simg` file. Absolute path to access to the container file fills the field `singularity:` into [config.yaml](config/)
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## Conda
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Softwares can be installed throught a conda environment. Each rule loads its own environment. Environment files are stored at `workflow/envs/obitools_envs.yaml`.
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