improve validation pipelines (#70)

jagedn · web-flow · commit 88474c965d7b · 2024-07-16T17:55:33.000+02:00
Signed-off-by: Jorge Aguilera &lt;jorge@edn.es&gt;
diff --git a/validation/README.md b/validation/README.md
@@ -41,7 +41,7 @@ The most important part of the configuration (`basic/nextflow.config`) are:
 
 ``` 
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 ```
 
@@ -85,8 +85,17 @@ you can test some pipelines from your terminal using the `--nfazure` argument
 
 - `./run-all.sh --skiplocal --nfazure` run only remote pipelines
 
+### Test published version
 
+In case you want to run the validation using a published version (for example, 0.1.2-edge3 release), you can run:
 
+```
+export NOMAD_PLUGIN_VERSION=0.1.2-edge3
+
+export NXF_PLUGINS_TEST_REPOSITORY="https://github.com/nextflow-io/nf-nomad/releases/download/0.1.2-edge3/nf-nomad-0.1.2-edge3-meta.json"
+
+./run-all.sh
+```
 
 ## Stop the cluster
 
@@ -95,4 +104,4 @@ cd validation
 sudo ./stop-nomad.sh
 ```
 
-This command try to clean and kill the nomad process unmounting temp folders created by the client
+This command tries to clean and kill the nomad process unmounting temp folders created by the client
diff --git a/validation/az-nomadlab/2-volumes.config b/validation/az-nomadlab/2-volumes.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/az-nomadlab/nextflow.config b/validation/az-nomadlab/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/basic/nextflow.config b/validation/basic/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/constraints/node-nextflow.config b/validation/constraints/node-nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/directives/nextflow.config b/validation/directives/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/multiple-volumes/2-volumes.config b/validation/multiple-volumes/2-volumes.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/multiple-volumes/3-volumes.config b/validation/multiple-volumes/3-volumes.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {
diff --git a/validation/stop-nomad.sh b/validation/stop-nomad.sh
@@ -3,4 +3,6 @@
 ./nomad system gc
 sleep 1
 df -h --output=target | grep nf-task | xargs sudo umount
-pkill -9 nomad
+pkill -9 nomad
+sleep 1
+rm -rf nomad_temp
diff --git a/validation/sun-nomadlab/nextflow.config b/validation/sun-nomadlab/nextflow.config
@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-nomad@latest'
+    id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
 }
 
 process {

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`plugins {`
`2`		`- id 'nf-nomad@latest'`
	`2`	`+ id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"`
`3`	`3`	`}`
`4`	`4`
`5`	`5`	`process {`