diff --git a/example-bonus/README.md b/example-bonus/README.md index 38f3b42..e68aefd 100644 --- a/example-bonus/README.md +++ b/example-bonus/README.md @@ -18,11 +18,11 @@ wave { fusion { enabled = true + exportStorageCredentials = true } docker { enabled = true - envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY' } ``` diff --git a/example-bonus/nextflow.config b/example-bonus/nextflow.config index a0deee0..edad128 100644 --- a/example-bonus/nextflow.config +++ b/example-bonus/nextflow.config @@ -4,11 +4,11 @@ wave { fusion { enabled = true + exportStorageCredentials = true } docker { enabled = true - envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY' } workDir = 's3://nextflow-ci/work' diff --git a/example-gke/nextflow.config b/example-gke/nextflow.config index 6adde09..9504760 100644 --- a/example-gke/nextflow.config +++ b/example-gke/nextflow.config @@ -19,5 +19,4 @@ k8s { namespace = 'wave-demo' serviceAccount = 'wave-sa' pod.nodeSelector = 'iam.gke.io/gke-metadata-server-enabled=true' - debug.yaml = true } diff --git a/example-googlebatch/nextflow.config b/example-googlebatch/nextflow.config index 6cb9194..68d0e16 100644 --- a/example-googlebatch/nextflow.config +++ b/example-googlebatch/nextflow.config @@ -6,7 +6,7 @@ params { process { executor = 'google-batch' - container = 'quay.io/nextflow/rnaseq-nf:v1.1' + container = 'quay.io/nextflow/rnaseq-nf:v1.2' scratch = true } diff --git a/example-spack/README.md b/example-spack/README.md index 4b31604..df6abd2 100644 --- a/example-spack/README.md +++ b/example-spack/README.md @@ -11,7 +11,6 @@ on-demand and provision for the pipeline execution. ``` docker { enabled = true - runOptions = '-u $(id -u):$(id -g)' } wave { diff --git a/example-spack/nextflow.config b/example-spack/nextflow.config index 1a36b3a..b5c9de5 100644 --- a/example-spack/nextflow.config +++ b/example-spack/nextflow.config @@ -1,6 +1,5 @@ docker { enabled = true - runOptions = '-u $(id -u):$(id -g)' } wave { diff --git a/example6/nextflow.config b/example6/nextflow.config index f588343..46af285 100644 --- a/example6/nextflow.config +++ b/example6/nextflow.config @@ -1,5 +1,5 @@ process { - container = 'quay.io/nextflow/rnaseq-nf:v1.1' + container = 'quay.io/nextflow/rnaseq-nf:v1.2' } params { @@ -9,11 +9,11 @@ params { docker { enabled = true - envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY' } fusion { enabled = true + exportStorageCredentials = true } workDir = 's3://nextflow-ci/wave' diff --git a/example7/README.md b/example7/README.md index 1090f31..b4dd89c 100644 --- a/example7/README.md +++ b/example7/README.md @@ -13,10 +13,6 @@ to provision the pipeline containers on-demand, by using the Conda recipes defin wave { enabled = true strategy = 'conda,container' - build.conda.commands = [ - 'USER root', - 'RUN apt-get update -y && apt-get install -y procps' - ] } docker { @@ -25,6 +21,7 @@ docker { fusion { enabled = true + exportStorageCredentials = true } ``` diff --git a/example7/nextflow.config b/example7/nextflow.config index 57db8b8..b46f9ca 100644 --- a/example7/nextflow.config +++ b/example7/nextflow.config @@ -1,19 +1,14 @@ -plugins { - id 'nf-wave' -} - wave { enabled = true strategy = 'conda,container' - build.conda.basePackages = 'conda-forge::procps-ng' } docker { enabled = true - envWhitelist = 'AWS_ACCESS_KEY_ID,AWS_SECRET_ACCESS_KEY' } fusion { enabled = true + exportStorageCredentials = true } diff --git a/example8/nextflow.config b/example8/nextflow.config index 3722a3a..be42fc1 100644 --- a/example8/nextflow.config +++ b/example8/nextflow.config @@ -11,7 +11,7 @@ k8s { process { executor = 'k8s' - container = 'quay.io/nextflow/rnaseq-nf:v1.1' + container = 'quay.io/nextflow/rnaseq-nf:v1.2' scratch = true }