Sync test resources

Synchronise the test resources from s3://openpipelines-data to resources_test

Info

ID: sync_test_resources
Namespace: download

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 1.0.1 -latest \
  -main-script target/nextflow/download/sync_test_resources/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: "s3://openpipelines-data"
# output: "$id.$key.output.output"
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 1.0.1 -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 group

Arguments

Name Description Attributes
--input Path to the S3 bucket to sync from. string, default: "s3://openpipelines-data"
--output Path to the test resource directory. file, default: "resources_test"
--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)