Sync test resources

Sync test resources to the local filesystem

Info

ID: sync_test_resources
Namespace: download

Links

Source

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -main-script target/nextflow/download/sync_test_resources/main.nf \
  --help

Run command

Example of params.yaml

# Inputs
input: "_viash.yaml"

# Outputs
# output: "."

# Arguments
quiet: false
dryrun: false
delete: false
# exclude: ["foo"]

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"

nextflow run openpipelines-bio/openpipeline \
  -r 2.1.0 -latest \
  -profile docker \
  -main-script target/nextflow/download/sync_test_resources/main.nf \
  -params-file params.yaml

Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name	Description	Attributes
--input	Path to the _viash.yaml project configuration file.	file, default: "_viash.yaml"

Outputs

Name	Description	Attributes
--output	Path to the directory where the resources will be synced to.	file, default: "."

Arguments

Name	Description	Attributes
--quiet	Displays the operations that would be performed using the specified command without actually running them.	boolean_true
--dryrun	Does not display the operations performed from the specified command.	boolean_true
--delete	Files that exist in the destination but not in the source are deleted during sync.	boolean_true
--exclude	Exclude all files or objects from the command that matches the specified pattern.	List of string, multiple_sep: ";"

Authors

• Robrecht Cannoodt (maintainer)