Viash Hub

Description

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

Arguments

Name	Type & Properties	Description
--base_dir	file required	Base directory to search recursively
--pattern	string required	An optional regular expression. Only file names which match the regular expression will be matched.
--n_dirname_drop	integer	For every matched file, the parent directory will be traversed N times.
--n_basename_id	integer	The unique identifiers will consist of at least N dirnames.
--id_name	string	The name for storing the identifier field in the yaml.
--path_name	string	The name for storing the path field in the yaml.
--group_name	string	Top level name for the group of entries.
--output	file required output	Output YAML file.

Name

Type & Properties

--base_dir

file

required

--pattern

string

required

--n_dirname_drop

integer

--n_basename_id

integer

--id_name

string

--path_name

string

--group_name

string

--output

file

required

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
n_dirname_drop: [ 0 ]  
n_basename_id: [ 0 ]  
id_name: [ "id" ]  
path_name: [ "path" ]  
output: "$id.$key.output.yaml"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.1 \  
  -main-script target/nextflow/files/make_params/main.nf \  
  -params-file params.yaml

Relationships

Used by

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No components use this component.

Current component

files/make_paramsopenpipeline 1.0.1

Uses

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