Nextflow pipeline running software centrifuge to detect reads mapping to microbial or viral references, and optionally software virusbreakend to detect viral integration
- 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
Type | Description |
---|---|
input_folder | Input folder with BAM or CRAM files |
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 |
nextflow run iarcbioinfo/metagenomics-nf --input_folder crams
Type | Description |
---|---|
*_centrifuge_report.tsv | Centrifuge summary reports per sample |
*_centrifuge_results.txt | Centrifuge output per sample |
*virusbreakend.vcf | Virusbreakend vcf file output |
Name | Description | |
---|---|---|
Nicolas Alcala* | [email protected] | Developer to contact for support |