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

:map

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

reads

:file

Fastq file(s) to deduplicate

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

meta2

:map

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

umi_file

:file

UMI file

Output

name:type
description
pattern

log

meta

:map

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

${prefix}.log

:file

Log file of humid, containing progress and errors

*.log

dedup

meta

:map

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

*_dedup*.fastq.gz

:file

Deduplicated Fastq file(s)

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

annotated

meta

:map

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

*_annotated*.fastq.gz

:file

Annotated Fastq file(s)

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

stats

meta

:map

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

${prefix}

:directory

Directory containing statistics file, use for multiqc.

${prefix}/

versions_humid

${task.process}

:string

The name of the process

humid

:string

The name of the tool

1.0.4

:string

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

humid

:string

The name of the tool

1.0.4

:string

The expression to obtain the version of the tool

Tools

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