You cannot select more than 25 topics
Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
38 lines
1.4 KiB
Markdown
38 lines
1.4 KiB
Markdown
# 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.
|
|
|
|
|
|
|
|
## Quick Start
|
|
|
|
```bash
|
|
GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
|
|
NXF_MODE=google
|
|
nextflow run nf-core/rnaseq -profile test,google --google_bucket <gs://your_bucket/work>
|
|
```
|
|
|
|
### Required Parameters
|
|
|
|
#### `--google_bucket`
|
|
|
|
The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
|
|
|
|
### Optional Parameters
|
|
|
|
#### `--google_zone`
|
|
|
|
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`
|
|
|
|
Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
|
|
|
|
#### `--google_debug`
|
|
|
|
Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
|
|
|
|
## Cloud Life Sciences Setup
|
|
|
|
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.
|