reads_bwamem2_decontamination
Description¶
Short-reads mapping to a reference genome and remove matching reads
Installation¶
ebi-metagenomics/reads_bwamem2_decontamination
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install reads_bwamem2_decontamination
Pipelines¶
This subworkflow is used by the following pipelines:
Components¶
This subworkflow uses the following components:
bwamem2/mem(module)samtools/bam2fq(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | - |
reads |
file | A list of input FastQ files of size 1 or 2 for single-end and paired-end data, respectively | *.{fastq/fq}.gz |
meta2 |
map | Groovy Map containing reference genome information e.g. [ id:'ref_name' ] | - |
ref_index |
file | A list of BWA index reference files | *.{amb,ann,bwt,pac,sa} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | - |
decont_reads |
file | A list of decontaminated FastQ files of size 1 or 2 for single-end and paired-end data, respectively | - |
versions |
file | File containing software versions | versions.yml |
