Changes between Version 1 and Version 2 of SOPs/nextflow

Timestamp:

03/25/25 15:01:50 (7 months ago)

Author:

xinlei.gao

Comment:

--

SOPs/nextflow

@@ -24 +24 @@
 
 == Installation of Nextflow
+Nextflow can be used on Linux, macOS and windows. It requires Bash 3.2 (or later) and Java 17 (or later, up to 23) to be installed.
+For the instructions to install Nextflow, please refer to this page: [https://www.nextflow.io/docs/latest/install.html]
 
+The Nextflow command line tool has been installed on the WI slurm cluster: /nfs/BaRC_Public/apps/nextflow/nextflow
+
+The current version is nextflow version 24.04.4.5917.
+
+The main purpose of the Nextflow CLI is to run Nextflow pipelines with the run command. Nextflow can execute a local script (e.g. ./main.nf) or a remote project (e.g. github.com/foo/bar).
+
+To launch the execution of a pipeline project, hosted in a remote code repository, you simply need to specify its qualified name or the repository URL after the run command. The qualified name is formed by two parts: the owner name and the repository name separated by a / character.
+
+In other words if a Nextflow project is hosted, for example, in a GitHub repository at the address http://github.com/foo/bar, it can be executed by entering the following command in your shell terminal:
+
+
+{{{
+nextflow run foo/bar
+}}}
+
+or using the project URL:
+
+
+{{{
+nextflow run http://github.com/foo/bar
+}}}
+
+If the project is found, it will be automatically downloaded to the Nextflow home directory ($HOME/.nextflow by default) and cached for subsequent runs.
+
+Try this simple example by running the following command:
+
+
+{{{
+nextflow run nextflow-io/hello
+}}}
+
+
+This is a simple script showing the basic 'Hello World!' example for the Nextflow framework. It will download a trivial example from the repository published at http://github.com/nextflow-io/hello and execute it on your computer.