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Adds sshImage and copyImage as params
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cgpu committed May 12, 2021
1 parent 13c1cc4 commit 1f7bc34
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Showing 2 changed files with 12 additions and 1 deletion.
9 changes: 8 additions & 1 deletion conf/google.config
Original file line number Diff line number Diff line change
@@ -1,10 +1,17 @@
params {
executor = 'google-lifesciences'
dataLocation = 'gs://lifebit-featured-datasets/pipelines/spammer-nf/input_files'

// Nextflow default values with correction so that all pulled from gcr.io
gls_copyImage = 'gcr.io/google.com/cloudsdktool/cloud-sdk:alpine'
gls_sshImage = 'gcr.io/cloud-genomics-pipelines/tools'
}

google {
lifeSciences.copyImage = 'gcr.io/google.com/cloudsdktool/cloud-sdk:alpine'
// both images must be hosted in gcr.io of using private ips (gls_usePrivateAddress true)
lifeSciences.copyImage = params.gls_copyImage
lifeSciences.sshImage = params.gls_sshImage

lifeSciences.bootDiskSize = params.gls_bootDiskSize
lifeSciences.preemptible = params.gls_preemptible
zone = params.zone
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4 changes: 4 additions & 0 deletions nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,10 @@ params {
zone = 'us-east1-b'
network = 'default'
subnetwork = 'default'

// values defined in conf/google.config
gls_copyImage = false
gls_sshImage = false
}

// Do not update the order because the values set in params scope will not be overwritten
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