iarcbioinfo/qualimap-nf
Sponsored OSS
Automated build for Qualimap-nf
Image
Languages & frameworks
Integration & delivery
Data science
0
2.1K
iarcbioinfo/qualimap-nf repository overview
Quality control of WGS/WES/target alignment data
Description
Perform quality control of WGS/WES/target alignment data.
Dependencies
- 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.
- 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.)
- 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.)
- 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 | Description | |
|---|---|---|
| Tiffany Delhomme | [email protected] | developer |
| Maxime Vallee | [email protected] | developer |
| Matthieu Foll | [email protected] | developer |
| Nicolas Alcala* | [email protected] | Developer to contact for support |
Tag summary
Content type
Image
Digest
Size
899.2 MB
Last updated
over 6 years ago
docker pull iarcbioinfo/qualimap-nfThis week's pulls
Pulls:
223
Last week