Description

HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs.

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

reads{:bash}

:file

Fastq file(s) to deduplicate

*.{fastq,fq,fastq.gz,fq.gz}

meta2{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

umi_file{:bash}

:file

UMI file

Output

name:type
description
pattern

log{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}.log{:bash}

:file

Log file of humid, containing progress and errors

*.log

dedup{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_dedup*.fastq.gz{:bash}

:file

Deduplicated Fastq file(s)

*.{fastq,fq,fastq.gz,fq.gz}

annotated{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_annotated*.fastq.gz{:bash}

:file

Annotated Fastq file(s)

*.{fastq,fq,fastq.gz,fq.gz}

stats{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}{:bash}

:directory

Directory containing statistics file, use for multiqc.

${prefix}/

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

included in
viralmetagenome
maintainer
Github user Joon-Klaps
get in touch
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