Description

Taxonomic meta-omics profiling using universal marker genes

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

reads{:bash}

:file

List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, respectively. Or the intermediate bam file mapped by bwa to the mOTUs database or the output bam file from motus profile. Or the intermediate mgc read counts table.

*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}

db{:bash}

:directory

mOTUs database downloaded by motus downloadDB

Output

name:type
description
pattern

out{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.out{:bash}

:file

Results with taxonomic classification of each read

*.out

bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.bam{:bash}

:file

Optional intermediate sorted BAM file from BWA

*.{bam}

mgc{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.mgc{:bash}

:file

Optional intermediate mgc read count table file saved with -M.

*.{mgc}

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

*.log{:bash}

:file

Standard error logging file containing summary statistics

*.log

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
taxprofiler
maintainer
Github user jianhong
get in touch
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