adding nextflow w batch sample

[thomasnyc]

adding the nextflow batch sample .

[jrossthomson]

Is there a better way to pass these variables? Manually editing the config file is a bit cumbersome. How about creating a template compatible with envsubst?

// nextflow.config.template
profiles {
'google-batch' {
params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
params.reads = 'gs://rnaseq-nf/data/ggal/gut_{1,2}.fq'
params.multiqc = 'gs://rnaseq-nf/multiqc'
process.executor = 'google-batch'
process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.1'

    workDir = 'gs://${GCP_BUCKET_NAME}/scratch'
    google.location = '${GCP_REGION}'
    google.project = '${GCP_PROJECT_ID}'
    google.batch.allowedLocations = ['regions/${GCP_REGION}']

    // Network configuration
    google.batch.network = 'global/networks/${GCP_NETWORK_NAME}'
    google.batch.subnetwork = 'regions/${GCP_REGION}/subnetworks/${GCP_SUBNET_NAME}'
}

}

[thomasnyc]

I updated the nextflow.config and also README.md Please review.

[jrossthomson]

You don't want to do the envsubst thing?

[thomasnyc]

Not planning to add since there is only one file to modify.