Make params

Looks for files in a directory and turn it in a params file.

Info

ID: make_params
Namespace: files

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 0.12.6 -latest \
  -main-script target/nextflow/files/make_params/main.nf \
  --help

Run command

Example of params.yaml
# Arguments
base_dir: # please fill in - example: "/path/to/dir"
pattern: # please fill in - example: "*.fastq.gz"
n_dirname_drop: 0
n_basename_id: 0
id_name: "id"
path_name: "path"
# group_name: "param_list"
# output: "$id.$key.output.yaml"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 0.12.6 -latest \
  -profile docker \
  -main-script target/nextflow/files/make_params/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
--base_dir Base directory to search recursively file, required, example: "/path/to/dir"
--pattern An optional regular expression. Only file names which match the regular expression will be matched. string, required, example: "*.fastq.gz"
--n_dirname_drop For every matched file, the parent directory will be traversed N times. integer, default: 0
--n_basename_id The unique identifiers will consist of at least N dirnames. integer, default: 0
--id_name The name for storing the identifier field in the yaml. string, default: "id"
--path_name The name for storing the path field in the yaml. string, default: "path"
--group_name Top level name for the group of entries. string, example: "param_list"
--output Output YAML file. file, required, example: "params.yaml"

Authors

  • Angela Oliveira Pisco (author)

  • Robrecht Cannoodt (maintainer, author)