This little wrapper is designed to be used with orchestrator systems (HPC, K8s) which have a designated copy queue or node.
- Nextflow
- Conda
NOTE If you plan to setup a basic server, then you can refer minimal-nextflow-setup
⚠️ Conda or local setup only: Due to the nature of mounting files in a container, which involves a lot of copy/symlinks overheads, this wrapper assumes that you are usingrcloneinstalled in a location shared across all nodes.
✔️ Please ensure that your
$HOME/.config/rclone/rclone.conffile is populated with the correct details of any remotes. For more information please refer the rclone documentation
nextflow pull https://github.com/nf-modules-hub/rclone
To transfer a specific file/folder from any source location to a target location, you can rely upon the source and target parameters.
nextflow run https://github.com/nf-modules-hub/rclone --source /path/to/source --target /path/to/target
To transfer a specific file/folder from any source location to a target location, you can rely upon the samplesheet parameter.
The structure of samplesheet is very minimal since it only requires source and target columns as shown below
source,target
/path/to/a_file,registered-remote:/destination/path/to/a_file
/path/to/a_folder,registered-remote:/destination/path/to/a_folder
Then refer that while invoking the pipeline
nextflow run https://github.com/nf-modules-hub/rclone --samplesheet /path/to/samplesheet
To customize these scripts, you can take a look at the available parameters in ./nextflow.config file and then override them using a local config file, in a directory where you'd like to launch the pipeline.
Please use the Github citation page to cite this wrapper in your research.
The sole purpose of process wrappers in nf-modules-hub is to keep the code small, clean and hackable with some basic knowledge of nextflow scripting.
If you have specific requirements, you are encouraged to fork/clone and update your version to accomodate your needs.
Contribution, in all forms, is most welcome!