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# bolero
bolero is a nextflow pipeline dedicated to analyse Nanopore sequencing coupled to 5'RACE amplification of HBV RNAs.
## Getting the last updates
To get the last commits from this repository into your fork use the following commands:
```sh
git clone git@gitbio.ens-lyon.fr:xgrand/bolero.git
```
## Getting Started
The pipeline `src/bolero.nf` works a nextflow configuration file `src/nextflow.config`.
The typical command for running the pipeline is as follows:
`nextflow ./src/bolero.nf -c ./src/nextflow.config -profile singularity`
The arguments of this pipeline are described in the table below:
| Arguments | Description |
|:---------------------------:|:-------------------------------------------------------------------:|
| -c | configuration file. This parameter should always be `src/nextflow.config` |
| -profile | The profile to use. This can be **docker** or **singularity** to run the pipeline in docker or singularity container respectively. This can also be **psmn** to launch the analysis on the PSMN |
| --input [path] | Path to the folder containing fast5 files. If skip basecalling option enabled, path to fastq files folder. |
| --adapt [str] | Sequence of 5'RACE adapter. |
| --genome [file] | Path to the fasta file containing the genome. |
| --gtf [file] | Path to the gtf file containing the genome annotation. |
| --skipBC [boolean] | Skip basecalling step. If truen give fastq folder as input. Default: true. |
| --flowcell [str] | Nanopore flowcell. Default = FLO-MIN106. |
| --kit [str] | Nanopore kit. Default = SQK-PBK004. |
| --gpu_mode [str] | Guppy basecaller configuration. Default: false.
"gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications. |
| --min_qscore [float] | Minimum quality score threshold, default = 7.0. |
| --gpu_runners_per_device [int] | Number of runner per device, default = 32 (refer to guppy manual). |
| --num_callers [int] | Number of callers, default = 16 (refer to guppy manual). |
| --chunks_per_runner [int] | Number of chunks per runner, default = 512 (refer to guppy manual). |
| --chunks_size [int] | Chunck size, default = 1900 (refer to guppy manual). |
| --help --h | Display this help message. |
## Contributing
If you want to add more tools to this project, please read the [CONTRIBUTING.md](CONTRIBUTING.md).
## Authors
* **Xavier Grand** - *Maintainer*
## License
This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) file for details
## To Do:
* Give the user the possibility to choose the basecalling configuration file