Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

improve validation pipelines #70

Merged
merged 1 commit into from
Jul 16, 2024
Merged

improve validation pipelines #70

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 11 additions & 2 deletions validation/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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"}"
}
```

Expand Down Expand Up @@ -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

Expand All @@ -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
2 changes: 1 addition & 1 deletion validation/az-nomadlab/2-volumes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
2 changes: 1 addition & 1 deletion validation/az-nomadlab/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
2 changes: 1 addition & 1 deletion validation/basic/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
2 changes: 1 addition & 1 deletion validation/constraints/node-nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
2 changes: 1 addition & 1 deletion validation/directives/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
2 changes: 1 addition & 1 deletion validation/multiple-volumes/2-volumes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
2 changes: 1 addition & 1 deletion validation/multiple-volumes/3-volumes.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
4 changes: 3 additions & 1 deletion validation/stop-nomad.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
2 changes: 1 addition & 1 deletion validation/sun-nomadlab/nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
plugins {
id 'nf-nomad@latest'
id "nf-nomad@${System.getenv("NOMAD_PLUGIN_VERSION") ?: "latest"}"
}

process {
Expand Down
Loading