First commit of Google Cloud config

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
+          profile: ['awsbatch', 'bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'ccga', 'cfc', 'crick', 'denbi_qbic', 'genotoul', 'genouest', 'gis', 'hebbe', 'google', 'kraken', 'munin', 'pasteur', 'phoenix', 'prince', 'shh', 'uct_hex', 'uppmax', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

README.md

@@ -108,6 +108,7 @@ Currently documentation is available for the following systems:
 * [GENOTOUL](docs/genotoul.md)
 * [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
+* [GOOGLE](docs/google.md)
 * [HEBBE](docs/hebbe.md)
 * [KRAKEN](docs/kraken.md)
 * [MUNIN](docs/munin.md)

conf/google.config

@@ -0,0 +1,21 @@
+// Nextflow config file for running on Google Cloud Life Sciences
+params {
+  config_profile_description = 'Google Cloud Life Sciences Profile'
+  config_profile_contact = 'Evan Floden, Seqera Labs (@evanfloden)'
+  config_profile_url = 'https://cloud.google.com/life-sciences'
+
+  google_zone = 'europe-west2-c'
+  google_bucket = false
+  google_debug = false
+  google_preemptible = true
+}
+
+process.executor = 'google-lifesciences'
+google.zone = params.google_zone
+google.lifeSciences.debug = params.google_debug
+workDir = params.google_bucket
+google.lifeSciences.preemptible = params.google_preemptible
+if (google.lifeSciences.preemptible) {
+  process.errorStrategy = { task.exitStatus==14 ? 'retry' : 'terminate' }
+  process.maxRetries = 5
+}

docs/google.md

@@ -0,0 +1,30 @@
+# nf-core/configs: Google Cloud Life Sciences Configuration
+![Google Cloud](images/google-cloud-logo.png "https://cloud.google.com/life-sciences/docs/tutorials/nextflow")
+
+To be used with the `google` profile by specifying the `-profile google` when running nf-core pipelines.
+
+## Quick Start
+```
+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`).
+
+## Google 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.
+
+

nfcore_custom.config

@@ -24,6 +24,7 @@ profiles {
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config";
                  includeConfig "${params.custom_config_base}/conf/czbiohub_aws_highpriority.config"}
   genotoul     { includeConfig "${params.custom_config_base}/conf/genotoul.config" }
+  google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   denbi_qbic   { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }