https://github.com/pwwang/biopipen
A set of processes/pipelines for bioinformatics
https://github.com/pwwang/biopipen
bioinformatics bioinformatics-pipeline bioinformatics-scripts pipeline-framework
Last synced: 3 months ago
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A set of processes/pipelines for bioinformatics
- Host: GitHub
- URL: https://github.com/pwwang/biopipen
- Owner: pwwang
- Created: 2017-02-10T15:43:29.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2025-01-02T19:18:47.000Z (4 months ago)
- Last Synced: 2025-01-09T18:35:44.444Z (4 months ago)
- Topics: bioinformatics, bioinformatics-pipeline, bioinformatics-scripts, pipeline-framework
- Language: R
- Homepage: https://pwwang.github.io/biopipen
- Size: 42.6 MB
- Stars: 13
- Watchers: 4
- Forks: 5
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
A set of processes/pipelines for bioinformatics based on
pipen
## Installation
```shell
pip install -U biopipen
```
## Usage
### Use as APIs
```python
from pipen import Proc, Pipen
from biopipen.ns.bed import BedLiftOver
MyBedLiftOver = Proc.from_proc(BedLiftOver)
if __name__ == "__main__":
Pipen().set_start(MyBedLiftOver).run()
```
### Use as pipen-cli-run plugin
```shell
❯ pipen run bed BedLiftOver --help
Usage: pipen [-h | -h+] [options]
Liftover a BED file using liftOver
Use `@configfile` to load default values for the options.
Pipeline Options:
--name NAME The name for the pipeline, will affect the default workdir and
outdir. [default: BedLiftOver_pipeline]
--profile PROFILE The default profile from the configuration to run the pipeline.
This profile will be used unless a profile is specified in the
process or in the .run method of pipen. You can check the available
profiles by running `pipen profile`
--outdir OUTDIR The output directory of the pipeline [default: ./_results]
--forks FORKS How many jobs to run simultaneously by the scheduler
--scheduler SCHEDULER
The scheduler to run the jobs
Namespace :
--envs ENVS Environment variables for the process [default: {'liftover':
'liftOver', 'chain': ''}]
--envs.liftover LIFTOVER
The path to liftOver [default: liftOver]
--envs.chain CHAIN The map chain file for liftover [default: ]
Namespace :
--in.inbed INBED [INBED ...]
The input BED file
Namespace :
--out.outbed OUTBED The output BED file [default: {{in.inbed | basename}}]
Options:
-h, --help, -h+, --help+
show help message (with + to show more options) and exit
```