You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: docs/hello_nextflow/seqera/01_run_with_cli.md
+27-22Lines changed: 27 additions & 22 deletions
Original file line number
Diff line number
Diff line change
@@ -6,7 +6,7 @@ Start by logging into the [Seqera Platform](https://cloud.seqera.io/).
6
6
!!! info "Nextflow Tower"
7
7
8
8
Seqera Platform was previously known as Nextflow Tower.
9
-
You'll still see references to the previous name in environment variable and cli option names.
9
+
You'll still see references to the previous name in environment variables and CLI option names.
10
10
11
11
### 1.1. Set up your Seqera Platform token by exporting it to your environment
12
12
@@ -26,21 +26,26 @@ Follow these steps to set up your token:
26
26
27
27
!!! note
28
28
29
-
Leave this browser tab open as we will need the token once more to store it as a Nextflow secret.
29
+
Leave the browser tab with the token open as we will need it once more to store it as a Nextflow secret.
30
30
31
31
4. To make your token available to the Nextflow CLI, export it on the command line:
32
32
33
33
Open a terminal and type:
34
34
35
35
```bash
36
-
export TOWER_ACCESS_TOKEN=eyxxxxxxxxxxxxxxxQ1ZTE=
36
+
export TOWER_ACCESS_TOKEN=eyxxxxxxxxxxxxxxxQ1ZTE=
37
37
```
38
38
39
39
Where `eyxxxxxxxxxxxxxxxQ1ZTE=` is the token you have just created.
40
40
41
-
### 1.2. Run Nextflow cli with Seqera Platform visualizing and capturing logs
41
+
!!! Warning "Security Note"
42
42
43
-
Run your Nextflow workflows as usual with the addition of the `-with-tower` command:
43
+
Keep your token secure and do not share it with others.
44
+
You can add a ++space++ before the `export`command to prevent it from being saved in your shell history.
45
+
46
+
### 1.2. Run Nextflow CLI with Seqera Platform visualizing and capturing logs
47
+
48
+
Run a Nextflow workflow with the addition of the `-with-tower` command:
44
49
45
50
```bash
46
51
nextflow run nextflow-io/hello -with-tower
@@ -66,7 +71,7 @@ Hola world!
66
71
Hello world!
67
72
```
68
73
69
-
Use ++ctrl+click++ or ++cmd+click++ on the link to open it in your browser.
74
+
Hold ++ctrl++ or ++cmd++ and click on the link to open it in your browser.
70
75
You'll see the Seqera Platform interface with the job finished and the logs captured.
71
76
72
77
@@ -75,40 +80,40 @@ You will see and be able to monitor your **Nextflow jobs** in Seqera Platform.
75
80
76
81
### 1.3. Set up Seqera Platform in Nextflow configuration
77
82
78
-
Doing that token setup regularly can get bit tedious, but the same setup can be applied in configuration applied to Nexflow configuration so that it does not need to be set each time.
79
-
This can be the `nextflow.config` file of a specific project, or the global file located at `$HOME/.nextflow/config`, which will apply to all your runs.
83
+
Doing that token setup regularly can get a bit tedious, so let's set this configuration for all our pipeline runs with the global Nextflow configuration file located at `$HOME/.nextflow/config`.
80
84
81
85
Before we set the configuration, we need to permanently store the token in Nextflow using a [Nextflow secret](https://www.nextflow.io/docs/latest/secrets.html):
82
86
83
87
```bash
84
88
nextflow secrets set tower_access_token "eyxxxxxxxxxxxxxxxQ1ZTE="
85
89
```
86
90
87
-
The following block of configuration will enable Seqera Platform logging by default:
91
+
Open the Nextflow configuration file located at `$HOME/.nextflow/config`:
88
92
89
-
```groovy title="nextflow.config"
90
-
tower {
91
-
enabled = true
92
-
endpoint = "https://api.cloud.seqera.io"
93
-
accessToken = secrets.tower_access_token
94
-
}
93
+
```bash
94
+
code $HOME/.nextflow/config
95
95
```
96
96
97
-
However, instead of enabling Seqera Platform for an individual pipeline, we want to enable it for ourselves globally.
98
-
99
-
Run the following command to put the config block in your user configuration file located at `$HOME/.nextflow/config`.
97
+
Then add the following block of configuration:
100
98
101
-
```bash
102
-
cat <<EOF >> $HOME/.nextflow/config
99
+
```groovy title="$HOME/.nextflow/config"
103
100
tower {
104
101
enabled = true
105
102
endpoint = "https://api.cloud.seqera.io"
106
103
accessToken = secrets.tower_access_token
104
+
workspaceId = secrets.tower_workspace_id
107
105
}
108
-
EOF
109
106
```
110
107
111
-
Run your Nextflow workflows as usual:
108
+
!!! hint "Workspace ID and Endpoint`
109
+
110
+
We haven't set `secrets.tower_workspace_id` yet, and so Nextflow will fill in an empty string for this value.
111
+
This will default to the user's workspace in Seqera Platform which is what we want for now.
112
+
113
+
The `endpoint` is the URL of the Seqera Platform API.
114
+
If your institution is running a private instance of Seqera Platform, you will want to change this to the appropriate URL.
115
+
116
+
Run your Nextflow workflows as before, but without the `-with-tower` command:
0 commit comments