1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-09-21 14:02:05 +00:00
nf-configs/docs/google.md

38 lines
1.4 KiB
Markdown
Raw Normal View History

2020-03-06 05:47:29 +00:00
# nf-core/configs: Google Cloud Life Sciences Configuration
To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
2020-03-06 05:58:59 +00:00
![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
2020-03-06 05:47:29 +00:00
## Quick Start
2020-03-06 10:27:44 +00:00
```bash
2020-03-06 05:47:29 +00:00
GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
NXF_MODE=google
2020-03-09 13:44:58 +00:00
nextflow run nf-core/rnaseq -profile test,google --google_bucket <gs://your_bucket/work>
2020-03-06 05:47:29 +00:00
```
2020-03-06 05:58:59 +00:00
### Required Parameters
2020-03-06 10:27:44 +00:00
#### `--google_bucket`
2020-03-06 10:27:44 +00:00
2020-03-06 05:47:29 +00:00
The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
2020-03-06 05:58:59 +00:00
### Optional Parameters
2020-03-06 10:27:44 +00:00
#### `--google_zone`
2020-03-06 10:27:44 +00:00
2020-03-06 05:47:29 +00:00
The Google zone where the computation is executed in Compute Engine VMs. Multiple zones can be provided separating them by a comma. Default (`europe-west2-c`).
#### `--google_preemptible`
2020-03-06 10:27:44 +00:00
2020-03-06 05:58:59 +00:00
Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
2020-03-06 05:47:29 +00:00
#### `--google_debug`
2020-03-06 05:47:29 +00:00
2020-03-06 10:27:44 +00:00
Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
2020-03-06 05:58:59 +00:00
## Cloud Life Sciences Setup
2020-03-06 05:47:29 +00:00
2020-03-06 10:27:44 +00:00
Please refer to the [Google Cloud](https://cloud.google.com/life-sciences/docs/tutorials/nextflow) and [Nextflow](https://www.nextflow.io/docs/latest/google.html#cloud-life-sciences) documentation which describe how to setup the Google Cloud environment.