Download file

Download a file

Info

ID: download_file
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 2.1.1 -latest \
  -main-script target/nextflow/download/download_file/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: "https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"
# output: "$id.$key.output.h5"
verbose: false

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 2.1.1 -latest \
  -profile docker \
  -main-script target/nextflow/download/download_file/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 URL to a file to download. string, required, example: "https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"
--output Path where to store output. file, required, example: "pbmc_1k_protein_v3_raw_feature_bc_matrix.h5"
--verbose Increase verbosity boolean_true

Authors

  • Robrecht Cannoodt (maintainer)