From dbd0ac7e128afba7891c3dea7fde5c582c4e7971 Mon Sep 17 00:00:00 2001 From: aliarifki <aliarifki@outlook.fr> Date: Wed, 31 May 2023 09:49:04 +0200 Subject: [PATCH] =?UTF-8?q?Mise=20=C3=A0=20jour=20du=20readme?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- README.md | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 31be413..acb4408 100755 --- a/README.md +++ b/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 -- GitLab