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37 lines
1.4 KiB
Markdown
37 lines
1.4 KiB
Markdown
# nf-core/configs: Google Cloud Life Sciences Configuration
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To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
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## Quick Start
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```bash
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GOOGLE_APPLICATION_CREDENTIALS=<your_key>.json
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NXF_MODE=google
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nextflow run nf-core/rnaseq -profile test,google --google_bucket <gs://your_bucket/work>
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```
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### Required Parameters
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#### `--google_bucket`
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The Google Cloud Storage bucket location to be used as a Nextflow work directory. Can also be specified with (`-w gs://your_bucket/work`).
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### Optional Parameters
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#### `--google_zone`
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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`).
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#### `--google_preemptible`
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Enables the usage of preemptible virtual machines with a retry error statergy for up to 5 retries. Default (`true`).
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#### `--google_debug`
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Copies the /google debug directory from the VM to the task bucket directory. Useful for debugging. Default (`false`).
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## Cloud Life Sciences Setup
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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.
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