A tool to estimate bacterial species abundance
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads{:bash}
:file
Reads in FASTQ format
*.{fastq.gz}
meta2{:bash}
Groovy Map containing database information e.g. [ id:‘test’]
db{:bash}
A database formatted for MIDAS
*.{db}
mode{:bash}
:string
The mode to run MIDAS is
*
results{:bash}
${prefix}/*{:bash}
A directory of results from MIDAS run
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
An integrated pipeline for estimating strain-level genomic variation from metagenomic data
