metagenomics-nf
April 20, 2024 ยท View on GitHub
Nextflow pipeline to perform metagenomic analyses from next-generation sequncing data
Description
Nextflow pipeline running software centrifuge to detect reads mapping to microbial or viral references, and optionally software virusbreakend to detect viral integration
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.
- External software:
You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.
To use virusbreakend, you will need to download the database. See help at https://github.com/PapenfussLab/gridss/blob/master/VIRUSBreakend_Readme.md
Input
| Type | Description |
|---|---|
| input_folder | Input folder with BAM or CRAM files |
Parameters
| Name | Default value | Description |
|---|---|---|
| --output_folder | metagenomics-nf_results | |
| --cpu | 2 | Number of CPUs |
| --mem | 8 | Memory in Gb |
| --ref | Host reference genome | |
| --virusbreakend_db | Virusbreakend database (e.g., virusbreakenddb_20210401 from https://github.com/PapenfussLab/gridss/blob/master/VIRUSBreakend_Readme.md) |
Flags are special parameters without value. The virusbreakend process will be triggered automatically if the virusbreakend_db parameter is specified.
| Name | Description |
|---|---|
| --help | Display help |
Usage
nextflow run iarcbioinfo/metagenomics-nf --input_folder crams
Output
| Type | Description |
|---|---|
| *_centrifuge_report.tsv | Centrifuge summary reports per sample |
| *_centrifuge_results.txt | Centrifuge output per sample |
| *virusbreakend.vcf | Virusbreakend vcf file output |
Contributions
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | alcalan@iarc.who.int | Developer to contact for support |