Skip to content
GitLab
Explore
Sign in
Primary navigation
Search or go to…
Project
B
bolero
Manage
Activity
Members
Labels
Plan
Issues
Issue boards
Milestones
Wiki
Code
Merge requests
Repository
Branches
Commits
Tags
Repository graph
Compare revisions
Snippets
Build
Pipelines
Jobs
Pipeline schedules
Artifacts
Deploy
Releases
Package registry
Model registry
Operate
Environments
Terraform modules
Monitor
Incidents
Analyze
Value stream analytics
Contributor analytics
CI/CD analytics
Repository analytics
Model experiments
Help
Help
Support
GitLab documentation
Compare GitLab plans
Community forum
Contribute to GitLab
Provide feedback
Keyboard shortcuts
?
Snippets
Groups
Projects
Show more breadcrumbs
Xavier Grand
bolero
Commits
dbd0ac7e
Commit
dbd0ac7e
authored
1 year ago
by
aliarifki
Browse files
Options
Downloads
Patches
Plain Diff
Mise à jour du readme
parent
f048b1cc
No related branches found
No related tags found
No related merge requests found
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
README.md
+14
-4
14 additions, 4 deletions
README.md
with
14 additions
and
4 deletions
README.md
+
14
−
4
View file @
dbd0ac7e
...
@@ -13,6 +13,8 @@ git clone git@gitbio.ens-lyon.fr:xgrand/bolero.git
...
@@ -13,6 +13,8 @@ git clone git@gitbio.ens-lyon.fr:xgrand/bolero.git
## Getting Started
## Getting Started
The pipeline
`src/bolero.nf`
works a nextflow configuration file
`src/nextflow.config`
.
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:
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:
...
@@ -24,11 +26,17 @@ The arguments of this pipeline are described in the table below:
| --adapt [str] | Sequence of 5'RACE adapter. |
| --adapt [str] | Sequence of 5'RACE adapter. |
| --genome [file] | Path to the fasta file containing the genome. |
| --genome [file] | Path to the fasta file containing the genome. |
| --gtf [file] | Path to the gtf file containing the genome annotation. |
| --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. |
| --flowcell [str] | Nanopore flowcell. Default = FLO-MIN106. |
| --kit [str] | Nanopore kit. Default = SQK-PBK004. |
| --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". |
| --gpu_mode [str] | Guppy basecaller configuration. Default: false.
| --skipBC [Boolean] | Skip basecalling step. If TRUE, give fastq folder as input. |
"gpu" mode is dedicated to NVIDIA Cuda compatible system according to Guppy specifications. |
| --help | Display this help message. |
| --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
## Contributing
...
@@ -45,4 +53,6 @@ This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) fi
...
@@ -45,4 +53,6 @@ This project is licensed under the CeCiLL License- see the [LICENSE](LICENSE) fi
## To Do:
## 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
This diff is collapsed.
Click to expand it.
Preview
0%
Loading
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Save comment
Cancel
Please
register
or
sign in
to comment