From ebf42ca1512ff32b1235a640054e249aac9afa92 Mon Sep 17 00:00:00 2001 From: Ben Sherman Date: Sat, 29 Apr 2023 11:18:23 -0500 Subject: [PATCH] Update CLI docs Signed-off-by: Ben Sherman Signed-off-by: Paolo Di Tommaso Co-authored-by: Paolo Di Tommaso --- docs/cli.md | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/docs/cli.md b/docs/cli.md index ed74a6bbe5..628685cbbd 100644 --- a/docs/cli.md +++ b/docs/cli.md @@ -18,7 +18,6 @@ Nextflow options use a single dash prefix, e.g. `-foo`. Do not confuse with doub Available options: - `-C` : Use the specified configuration file(s) overriding any defaults. @@ -647,7 +646,6 @@ The `kuberun` command builds upon the `run` command and offers a deep integratio **Options** - `-E` : Exports all current system environment. @@ -1066,7 +1064,6 @@ The `run` command is used to execute a local pipeline script or remote pipeline **Options** - `-E` : Exports all current system environment. @@ -1132,7 +1129,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline : Comma separated list of plugin ids to be applied in the pipeline execution. `-process.=` -: Set process options. +: Set process config options. `-profile` : Choose a configuration profile. @@ -1209,7 +1206,7 @@ The `run` command is used to execute a local pipeline script or remote pipeline **Examples** -- Run a specific revision of a downloaded pipeline. +- Run a specific revision of a remote pipeline. ```console $ nextflow run nextflow-io/hello -r v1.1 @@ -1224,13 +1221,13 @@ The `run` command is used to execute a local pipeline script or remote pipeline $ nextflow run main.nf -profile docker ``` -- Invoke the pipeline execution and generate the summary HTML report. For more information on the metrics, please refer the {ref}`tracing-page` section: +- Execute a pipeline and generate the summary HTML report. For more information on the metrics, please refer the {ref}`tracing-page` section: ```console $ nextflow run main.nf -with-report ``` -- Invoke the nextflow pipeline execution with a custom queue size. By default, the queue size is the number of available CPUs. +- Execute a pipeline with a custom queue size. By default, the queue size is the number of available CPUs. ```console $ nextflow run nextflow-io/hello -qs 4 @@ -1242,19 +1239,19 @@ The `run` command is used to execute a local pipeline script or remote pipeline $ nextflow run nextflow-io/hello -dsl2 ``` -- Invoke the pipeline with a specific workflow as the entry-point, this option is meant to be used with DSL-2. For more information on DSL-2, please refer to {ref}`dsl2-page` +- Execute a pipeline with a specific workflow as the entry-point, this option is meant to be used with DSL-2. For more information on DSL-2, please refer to {ref}`dsl2-page` ```console $ nextflow run main.nf -entry workflow_A ``` -- Invoke the nextflow pipeline execution with the integrated monitoring in [Tower](https://cloud.tower.nf). +- Execute a pipeline with integrated monitoring in [Tower](https://cloud.tower.nf). ```console $ nextflow run nextflow-io/hello -with-tower ``` -- Invoke the nextflow pipeline execution with a custom parameters file (YAML or JSON). +- Execute a pipeline with a custom parameters file (YAML or JSON). ```console $ nextflow run main.nf -params-file pipeline_params.yml