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:
git clone git@gitbio.ens-lyon.fr:xgrand/bolero.gitGetting 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.
Authors
- Xavier Grand - Maintainer
- Alia Rifki - Contributor
License
This project is licensed under the CeCiLL License- see the LICENSE file for details
To Do:
- Give the user the possibility to choose the basecalling configuration file
- Change jpg to png in Start_positions.R
- Correct seqkit concatenate