Quality control of WGS/WES/target alignment data

Description

Perform quality control of WGS/WES/target alignment data.

Dependencies

1. This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
2. samtools: see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)
3. Qualimap: see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)
4. Multiqc: see official installation here. You can avoid installing all the external software by only installing Docker (not available yet). See the IARC-nf repository for more information.)

Input

Name	Description
--input_folder	Folder containing Fasta files

Parameters

Optional

Name	Default value	Description
--output_folder	.	Path to output folder
--qualimap	/usr/bin/qualimap	Path to Qualimap installation directory
--feature_file	myfeatures.txt	Qualimap feature file for coverage analysis
--multiqc_config	null	config yaml file for multiqc
--cpu	INTEGER	Number of cpus to be used

Flags

Flags are special parameters without value.

Name	Description
--help	Display help

Download test data set

git clone https://github.com/iarcbioinfo/data_test

Usage

nextflow run iarcbioinfo/Qualimap-nf --qualimap /path/to/qualimap --input_folder /path/to/bam --output_folder /path/to/output

Output

Name	Description
HTMLs	An html file for each analysed BAM file, and one containing the aggregated multiQC results

Contributions

Name	Email	Description
Tiffany Delhomme	Delhommet@students.iarc.fr	developer
Maxime Vallee	Valleem@iarc.fr	developer
Matthieu Foll	Follm@iarc.fr	developer
Nicolas Alcala*	AlcalaN@fellows.iarc.fr	Developer to contact for support