From e3c35db81af9491824af90942aa7cf5bf99c2bf1 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Wed, 10 Jan 2024 16:06:40 +0200 Subject: [PATCH 1/4] Update usage permissions Launch pipeline admonition: Launch users cannot add a new pipeline or run from a pipeline repo URL. --- USAGE.md | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/USAGE.md b/USAGE.md index a8467ae5..9b56838e 100644 --- a/USAGE.md +++ b/USAGE.md @@ -121,11 +121,11 @@ $ tw compute-envs import --name=my_aws_ce_v1 ./my_aws_ce_v1.json ## Pipelines -A Pipeline is composed of a workflow repository, launch parameters, and a Compute Environment. Pipelines are used to define frequently used pre-configured workflows in a Workspace. +A Pipeline is composed of a workflow repository, launch parameters, and a Compute Environment. Pipelines are used to define pre-configured workflows in a Workspace. ### Adding a Pipeline -Add a pre-configured Pipeline to the Launchpad that can be re-used later: +Add a pre-configured pipeline to the Launchpad that can be re-used later: ```console $ tw pipelines add --name=my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params.yaml https://github.com/nextflow-io/rnaseq-nf @@ -133,13 +133,13 @@ $ tw pipelines add --name=my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipel New pipeline 'my_rnaseq_nf_pipeline' added at user workspace ``` -The `--params-file` option was used to pass a set of default parameters that will be associated with the Pipeline in the Launchpad. +The `--params-file` option was used to pass a set of default parameters that will be associated with the pipeline in the Launchpad. > **NOTE**: The `params-file` option should be a YAML or JSON file. -### Importing/exporting a Pipeline +### Importing/exporting a pipeline -It is possible to export the configuration details for a Pipeline in JSON format for scripting and reproducibility purposes. +You can export the configuration details of a pipeline in JSON format for scripting and reproducibility purposes. ```console $ tw pipelines export --name=my_rnaseq_nf_pipeline my_rnaseq_nf_pipeline_v1.json @@ -147,7 +147,7 @@ $ tw pipelines export --name=my_rnaseq_nf_pipeline my_rnaseq_nf_pipeline_v1.json Pipeline exported into 'my_rnaseq_nf_pipeline_v1.json' ``` -Similarly, a Pipeline can easily be imported into a Workspace from a previously exported JSON file. +Similarly, a pipeline can easily be imported into a Workspace from a previously exported JSON file. ```console $ tw pipelines import --name=my_rnaseq_nf_pipeline_v1 ./my_rnaseq_nf_pipeline_v1.json @@ -155,7 +155,7 @@ $ tw pipelines import --name=my_rnaseq_nf_pipeline_v1 ./my_rnaseq_nf_pipeline_v1 New pipeline 'my_rnaseq_nf_pipeline_v1' added at user workspace ``` -### Updating a Pipeline +### Updating a pipeline The default launch parameters can be changed using the `update` command: @@ -163,11 +163,13 @@ The default launch parameters can be changed using the `update` command: tw pipelines update --name=my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params_2.yaml ``` -## Launching Pipelines +## Launching pipelines -### Launching a preconfigured Pipeline +### Launching a preconfigured pipeline -When launching a Pipeline from the Launchpad, if no custom parameters are passed via the CLI then the defaults set for the Pipeline in the Launchpad will be used. +When launching a pipeline from the Launchpad, if no custom parameters are passed via the CLI then the defaults set for the pipeline in the Launchpad will be used. + +> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launchpad users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines. ```console $ tw launch my_rnaseq_nf_pipeline @@ -184,9 +186,9 @@ When using `--wait`, `tw` can exit with one of two exit codes: > **TIP**: Use `--wait=SUCCEEDED` if you want the command to wait until the Pipeline execution is complete. -### Launching a Pipeline with custom parameters +### Launching a pipeline with custom parameters -Launch the Pipeline with different parameters +To launch the pipeline with different parameters: ```console $ tw launch my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params_2.yaml @@ -196,9 +198,9 @@ $ tw launch my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipeline_params_2.y https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx ``` -### Launching any Pipeline +### Launching any pipeline -It is also possible to directly launch Pipelines that have not been explicitly added to the Launchpad in a Tower Workspace by using the full Pipeline repository URL: +Platform CLI can directly launch pipelines that have not been explicitly added to the Launchpad in a platform workspace by using the full pipeline repository URL: ```console $ tw launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_params.yaml --compute-env=my_aws_ce --revision 3.8.1 --profile=test,docker @@ -208,11 +210,13 @@ $ tw launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_para https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx ``` +> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launchpad users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines. + In the above command: - Pipeline level parameters are defined within the `custom_rnaseq_params.yaml` file - Other parameters such as `--profile` and `--revision` can also be specified -- A non-primary Compute Environment has been used to launch the Pipeline +- A non-primary Compute Environment has been used to launch the pipeline ## Workspaces From 8fbfa470c5448cd6bcfd7e70d41923dd4b4d22d8 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Wed, 10 Jan 2024 16:10:34 +0200 Subject: [PATCH 2/4] Update USAGE.md --- USAGE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/USAGE.md b/USAGE.md index 9b56838e..43804a11 100644 --- a/USAGE.md +++ b/USAGE.md @@ -121,7 +121,7 @@ $ tw compute-envs import --name=my_aws_ce_v1 ./my_aws_ce_v1.json ## Pipelines -A Pipeline is composed of a workflow repository, launch parameters, and a Compute Environment. Pipelines are used to define pre-configured workflows in a Workspace. +A pipeline consists of a workflow repository, launch parameters, and a Compute Environment. Pipelines are used to define pre-configured workflows in a Workspace. ### Adding a Pipeline From 201768931eec70a7d26960a621a2bf15ff74f584 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Thu, 11 Jan 2024 14:27:11 +0200 Subject: [PATCH 3/4] Update USAGE.md --- USAGE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/USAGE.md b/USAGE.md index 43804a11..7380a8a4 100644 --- a/USAGE.md +++ b/USAGE.md @@ -210,7 +210,7 @@ $ tw launch https://github.com/nf-core/rnaseq --params-file=./custom_rnaseq_para https://tower.nf/user/abhinav/watch/2XDXxX0vCX8xhx ``` -> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launchpad users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines. +> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launch users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines. In the above command: From 77474429792e4252b4ba3b4738450e5adc7181e0 Mon Sep 17 00:00:00 2001 From: Llewellyn vd Berg <113503285+llewellyn-sl@users.noreply.github.com> Date: Thu, 11 Jan 2024 14:27:17 +0200 Subject: [PATCH 4/4] Update USAGE.md --- USAGE.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/USAGE.md b/USAGE.md index 7380a8a4..c55f4499 100644 --- a/USAGE.md +++ b/USAGE.md @@ -169,7 +169,7 @@ tw pipelines update --name=my_rnaseq_nf_pipeline --params-file=my_rnaseq_nf_pipe When launching a pipeline from the Launchpad, if no custom parameters are passed via the CLI then the defaults set for the pipeline in the Launchpad will be used. -> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launchpad users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines. +> **NOTE**: Platform CLI users are bound to the same user permissions that apply in the platform UI. Launch users can launch pre-configured pipelines in the workspaces they have access to, but they cannot add or run new pipelines. ```console $ tw launch my_rnaseq_nf_pipeline