Mise à jour du readme

README.md

@@ -13,6 +13,8 @@ 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:
 
@@ -24,11 +26,17 @@ The arguments of this pipeline are described in the table below:
 | --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. |
-| --mode [str] | Configuration to Guppy basecaller. Available: cpu, gpu. "gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications, default "cpu". |
-| --skipBC [Boolean] | Skip basecalling step. If TRUE, give fastq folder as input. |
-| --help | Display this help message. |
+| --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
 
@@ -45,4 +53,6 @@ This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) fi
 
 ## To Do:
 
-Give the user the possibility to choose the basecalling configuration file.
+* Give the user the possibility to choose the basecalling configuration file
+* Change jpg to png in Start_positions.R
+* Correct seqkit concatenate