millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 00:26:03 +00:00
Code Issues Releases Packages Activity

Update google.md or markdown linting

Browse source
This commit is contained in:
Evan Floden 2020-03-06 11:27:44 +01:00 committed by GitHub
parent 44cd3089de
commit f5364e45e7
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 9 additions and 6 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

15
docs/google.md
View file

@ -2,33 +2,36 @@
To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
![Google Cloud](images/google-cloud-logo.svg "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
## Quick Start
```
```bash
GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
NXF_MODE=google
nextflow run nf-core/rnaseq -profile google,test --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.