diff --git a/docs/hello_nextflow/seqera/01_run_with_cli.md b/docs/hello_nextflow/seqera/01_run_with_cli.md index f02ac6af..0a977e90 100644 --- a/docs/hello_nextflow/seqera/01_run_with_cli.md +++ b/docs/hello_nextflow/seqera/01_run_with_cli.md @@ -69,7 +69,11 @@ You will see and be able to monitor your **Nextflow jobs** in Seqera Platform. ### 1.3. Set up Seqera Platform in Nextflow configuration -Doing that token setup regularly can become tedious, so let's set this configuration for all our pipeline runs with the global Nextflow configuration file located at `$HOME/.nextflow/config`. +Doing that token setup regularly can become tedious, so let's set this configuration for all our pipeline runs with the global Nextflow configuration file located at `$NXF_HOME/.nextflow/config`. + +!!! hint "Home directory configuration" + + If `NFX_HOME` is not set, these changes would be added to `$HOME/.nextflow/config` Before we set the configuration, we need to permanently store the token from our environment in Nextflow using a [Nextflow secret](https://www.nextflow.io/docs/latest/secrets.html): @@ -83,15 +87,15 @@ Make sure your token was saved using: nextflow secrets get tower_access_token ``` -Next, open the Nextflow configuration file located at `$HOME/.nextflow/config`: +Next, open the Nextflow configuration file located at `$NXF_HOME/.nextflow/config`: ```bash -code $HOME/.nextflow/config +code $NXF_HOME/.nextflow/config ``` Then add the following block of configuration: -```groovy title="$HOME/.nextflow/config" +```groovy title="$NXF_HOME/.nextflow/config" tower { enabled = true endpoint = "https://api.cloud.seqera.io" @@ -113,14 +117,14 @@ nextflow run nextflow-io/hello You will see the following output: ```console title="Output" - N E X T F L O W ~ version 24.10.2 + N E X T F L O W ~ version 24.10.3 -Launching `https://github.com/seqeralabs/nf-hello-world` [scruffy_banach] DSL2 - revision: 8274d3d10c [master] +Launching `https://github.com/seqeralabs/nf-hello-world` [golden_moriondo] DSL2 - revision: 8274d3d10c [master] -Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/jonathan-manning2/watch/1Z3Jl1AXYRqXNx +Monitor the execution with Seqera Platform using this URL: https://cloud.seqera.io/user/jonathan-manning2/watch/1lzYhUz4ziHcYD executor > local (6) -[47/93f584] process > sayHello (2) [100%] 3 of 3 ✔ -[2a/0dc4a3] process > convertToUpper (3) [100%] 3 of 3 ✔ +[30/30a42c] process > sayHello (3) [100%] 3 of 3 ✔ +[ea/293e98] process > convertToUpper (3) [100%] 3 of 3 ✔ ``` Note that we are logging to Seqera Platform even though we did not use the `-with-tower` command! @@ -134,8 +138,8 @@ If you ran your pipeline from the `hello_nextflow` directory, you'll see somethi Notice that configuration for our pipeline run is being run pulled from three separate files: -- `/home/gitpod/.nextflow/config` - This is the global configuration file we just added. -- `/home/gitpod/.nextflow/assets/nextflow-io/hello/nextflow.config` - This is the `nextflow.config` file from the `nextflow-io/hello` repository. +- `/workspace/gitpod/.nextflow/config` - This is the global configuration file we just added. +- `/workspace/gitpod/.nextflow/assets/seqeralabs/nf-hello-world/nextflow.config` - This is the `nextflow.config` file from the `seqeralabs/nf-hello-world` repository. - `/workspace/gitpod/nf-training/hello-nextflow/nextflow.config` - This is the `nextflow.config` file from our current working directory. Nextflow resolves these configurations at runtime with a [specific order of precedence](https://www.nextflow.io/docs/latest/config.html#configuration-file). diff --git a/docs/hello_nextflow/seqera/img/resolved_configuration.png b/docs/hello_nextflow/seqera/img/resolved_configuration.png index 01ae3e54..cab53283 100644 Binary files a/docs/hello_nextflow/seqera/img/resolved_configuration.png and b/docs/hello_nextflow/seqera/img/resolved_configuration.png differ