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# legiolist-pre-processing

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Workflow that takes raw legiolist data and process it to be integrated in a legiolist intermine instance

## Running


### From gitlab

You can let nextflow cloning the workflow directly from gitlab.
To do that you need to configure the scm.
Create the file `$HOME/.nextflow/scm` with : 
```
providers {
    pasteur {
        server = 'https://gitlab.pasteur.fr'
        platform = 'gitlab'
    }
}
```

then you can directly run the workflow using :
```sh
nextflow run genolist/legiolist-pre-processing \
-hub pasteur \
--genome "/path/to/genomes/*"
```

Nextflow will clone the repo and run it automatically.

- You can list the workflow install with the command:
```sh
$ nextflow list
nf-core/rnaseq
genolist/legiolist-pre-processing
```

- Pull the last version
```sh
nextflow pull genolist/legiolist-pre-processing
```

- Delete the workflow
```sh
nextflow drop genolist/legiolist-pre-processing
```

### conda

```sh
nextflow run genolist/legiolist-pre-processing \
-hub pasteur \
--genome "/path/to/genomes/*" \
-profile conda
```

### docker

```sh
nextflow run genolist/legiolist-pre-processing \
-hub pasteur \
--genome "/path/to/genomes/*" \
-profile docker
```

### singularity

```sh
nextflow run genolist/legiolist-pre-processing \
-hub pasteur \
--genome "/path/to/genomes/*" \
-profile singularity
```


### On the cluster


- Load the modules:
```sh
module load java singularity
```


- Run the workflow (You need the create the scm file )
```sh
nextflow run genolist/legiolist-pre-processing \
-hub pasteur \
--genome "/path/to/genomes/*" \
-profile singularity,cluster
```
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### Issues

[cluster java version](https://github.com/nextflow-io/nextflow/blob/master/README.md#known-compilation-problems)