Tar extract

Extract files from a tar archive

Info

ID: tar_extract
Namespace: compression

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/compression/tar_extract/main.nf \
  --help

Run command

Example of params.yaml 
# Arguments
input: # please fill in - example: "input.tar.gz"
# output: "$id.$key.output"
# strip_components: 1
# exclude: "docs/figures"

# 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/compression/tar_extract/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 Input file file, required, example: "input.tar.gz"
--output Folder to restore file(s) to. file, required, example: "output_folder"
--strip_components Strip this amount of leading components from file names on extraction. For example, to extract only ‘myfile.txt’ from an archive containing the structure this/goes/deep/myfile.txt', use 3 to strip 'this/goes/deep/'. |integer, example:1| |–exclude|Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted. |string, example:“docs/figures”`