Update examples

Signed-off-by: Paolo Di Tommaso <[email protected]>
seqeralabs · Oct 13, 2023 · f4a38f7 · f4a38f7
1 parent 56eba4c
commit f4a38f7
Show file tree

Hide file tree

Showing 10 changed files with 8 additions and 19 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -1,6 +1,5 @@
 docker {
   enabled = true
-  runOptions = '-u $(id -u):$(id -g)'
 }
 
 wave {

diff --git 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
@@ -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
@@ -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
@@ -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
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,7 +11,6 @@ on-demand and provision for the pipeline execution. @@
     ```
     docker {
       enabled = true
-      runOptions = '-u $(id -u):$(id -g)'
     }
     wave {
@@ Expand Down @@