Skip to content

decompress.md

Latest commit

 

History

History
44 lines (29 loc) · 2.04 KB

decompress.md

File metadata and controls

44 lines (29 loc) · 2.04 KB
Raw

DECOMPRESS

Extract compressed archive files into Bruker .d directories.

Description

DECOMPRESS extracts compressed archive files (tar.gz, gz, tar, zip) into .d directories (Bruker timsTOF format). It includes tar verification after extraction and uses a retry strategy with escalating stageInMode (symlink to copy on AWS Batch, link to symlink to copy locally). Used within the FILE_PREPARATION subworkflow for handling compressed Bruker raw files.

Inputs

Channel Type Description
meta val(map) Sample metadata map (uses meta.mzml_id)
compressed_file path Compressed archive file (.tar.gz, .gz, .tar, .zip)

Outputs

Channel Type Description
decompressed_files tuple(meta, path) Decompressed .d directory
versions path Software versions (versions.yml) for gunzip, tar, unzip
log path Decompression log file

Parameters

Parameter Default Description
ext.prefix meta.mzml_id Override for the log file prefix

Container

quay.io/biocontainers/mulled-v2-796b0610595ad1995b121d0b85375902097b78d4:a3a3220eb9ee55710d743438b2ab9092867c98c6-0

Usage

Used in the FILE_PREPARATION subworkflow (subworkflows/local/file_preparation/main.nf) to decompress Bruker .d archives before downstream processing. Compressed files are branched and routed through DECOMPRESS, then mixed back with uncompressed files.

References