Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/heuermh/bdg-nextflow
Workflows implemented via Nextflow. Apache 2 licensed.
https://github.com/heuermh/bdg-nextflow
Last synced: 9 days ago
JSON representation
Workflows implemented via Nextflow. Apache 2 licensed.
- Host: GitHub
- URL: https://github.com/heuermh/bdg-nextflow
- Owner: heuermh
- License: apache-2.0
- Created: 2015-07-29T22:19:35.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2021-03-22T14:04:20.000Z (over 3 years ago)
- Last Synced: 2024-05-02T00:29:48.530Z (6 months ago)
- Language: Nextflow
- Homepage:
- Size: 18.6 KB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# bdg-nextflow
Workflows implemented via Nextflow.
### Hacking bdg-nextflow
Install
* JDK 1.8 or later, http://openjdk.java.net
* Nextflow version 0.16.1 or later, http://nextflow.io
```bash
$ curl -fsSL get.nextflow.io | bash
N E X T F L O W
Version 0.20.1 build 3853
last modified 18-06-2016 07:00 UTC (03:00 EDT)
http://nextflow.io
Nextflow installation completed.
```
### transform.nf
Transform all the BAM files found recursively in a given directory to ADAM format.
Run workflow locally (requires ADAM and dependencies to be installed locally)
```bash
$ ./nextflow run transform.nf
N E X T F L O W ~ version 0.20.1
Launching transform.nf
[warm up] executor > local
[fc/e23ff5] Submitted process > transform (foo)
[1a/7ed6a3] Submitted process > transform (bar)
$ ./nextflow run transform.nf --dir /my/directory/full/of/bam/files
...
```
Run workflow locally using Docker image such as [heuermh/adam](https://registry.hub.docker.com/u/heuermh/adam/) (requires only Docker to be installed locally)
```bash
$ ./nextflow run transform.nf -with-docker heuermh/adam
N E X T F L O W ~ version 0.20.1
Launching transform.nf
[warm up] executor > local
[89/75c6ac] Submitted process > transform (foo)
[f9/5bd7a8] Submitted process > transform (bar)
```
Use [SLURM](https://computing.llnl.gov/linux/slurm/) executor, with or without Docker
```bash
$ echo "process.executor = 'slurm'" > nextflow.config
$ ./nextflow run transform.nf
N E X T F L O W ~ version 0.20.1
Launching transform.nf
[warm up] executor > slurm
[f2/ba2eac] Submitted process > transform (bar)
[6a/40187f] Submitted process > transform (foo)
```