blcdsdockerregistry/pipeval repository overview

⁠PipeVal

⁠specs

⁠function:

Files (bam, vcf, fasta, bed, python)

• Existence of file at given path
• File extension type
• Validity of file for specific file type (i.e. a vcf file is a vcf file)
• Checksums (generates checksum comparison if .md5 or .sha512 file exists)

Directories (read or read-write)

• Existence of directory at given path
• Readability, writability

⁠input types:

The validation action can be specified using the -t tag. If not specified, it defaults to file-input.

If an input type is specified as "file-input", it will automatically try to match the file type or simply check for existence/readability. If an input type is one of the checksum types, it will create a new checksum file based on the input file path. All input types regardless will be checked for existence.

⁠requirements:

When used as a standalone command line tool, the following dependencies must be installed:

Otherwise, it's recommended to use the docker to keep dependencies bundled.

⁠usage

⁠parameters:

Required arg

• path path of one or more files or directories to validate or generate checksum for

Optional args

• -t, --type specific input type
• -h, --help show this help message and exit

⁠how to use:

Running the standalone command line tool

validate -t file-bam path/to/file.bam

Running as interactive docker session

docker run -it validate:1.0.0 /bin/bash
(bash): validate -t file-input path/to/file.bam

Running as Nextflow process with docker

check the example under /example/ or the pipeline-align-DNA repository

⁠usage commands:

⁠file specific validation

Currently file type specific validation is supported for the following:

To explicitly check a single file type, run

validate -t file-py path/to/file.py

Where file-py can be replaced with any file type listed in the input types table. To automatically detect any or multiple file types, run

validate -t file-input path/to/file.ext

The tool will try to automatically detect the file type and do file specific validation, and if the file type is unsupported, will just do a simple existence check.

⁠directory specific validation

To run validation for checking basic directory permissions you can run the following

validate -t directory-rw path/to/directory/

validate -t directory-r path/to/directory/

Using "directory-r" for read permissions, and "directory-rw" for read and write permissions.

⁠checksum generation (beta)

To generate a sha512 or md5 checksum file using this tool, run the following

validate -t md5-gen path/to/file.ext

validate -t sha512-gen path/to/file.ext

It should create a checksum file at the path/to/file.ext.{checksum_ext}

(TBD: Checksum comparison function still under development)

⁠output:

Valid input

Input: path/to/input is valid

Invalid input or error

Error: path/to/input Error Message

If the input is invalid in any way, validate will sys.exit and throw an exception which can be detected by Nextflow and handled accordingly.

⁠references:

Initial design: https://uclahs.box.com/s/eejwmwmdky7wsfcrs8a3jijy70rh6atp⁠

⁠license:

Author: Gina Kim ([email protected]⁠), Arpi Beshlikyan ([email protected]⁠)

PipeVal is licensed under the GNU General Public License version 2. See the file LICENSE for the terms of the GNU GPL license.

PipeVal is a tool which can be used to validate the inputs and outputs of various bioinformatic pipelines.

Copyright (C) 2020-2022 University of California Los Angeles ("Boutros Lab") All rights reserved.

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.