bwamem2decontnobams
Description¶
Decontamination module using bwamem2 and samtools that generates fastq files on the fly
Pipelines¶
This module is used by the following pipelines:
Installation¶
ebi-metagenomics/bwamem2decontnobams
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install bwamem2decontnobams
Tools¶
bwamem2¶
Mapping DNA sequences against a large reference genome
samtools¶
Tools for dealing with SAM, BAM and CRAM files
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
reads |
file | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively | - |
meta2 |
map | Groovy Map containing reference genome information e.g. [ id:'ref_name' ] | - |
index |
file | A list of BWA index files | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ] |
- |
versions |
file | File containing software versions | versions.yml |
decont_reads |
file | List of fastq files. Two files for paired-end reads and one file for single-end reads | - |
