Description

Taxonomic meta-omics profiling using universal marker genes

Input

name:type
description
pattern

meta

:map

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

reads

: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

:directory

mOTUs database downloaded by motus downloadDB

Output

name:type
description
pattern

out

meta

:map

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

*.out

:file

Results with taxonomic classification of each read

*.out

bam

meta

:map

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

*.bam

:file

Optional intermediate sorted BAM file from BWA

*.{bam}

mgc

meta

:map

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

*.mgc

:file

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

*.{mgc}

log

meta

:map

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

*.log

:file

Standard error logging file containing summary statistics

*.log

versions

versions.yml

:file

File containing software versions

versions.yml