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 containg statistics file, use for multiqc.

${prefix}/

versions

versions.yml:file

File containing software versions

versions.yml

Tools

maintainer
Github user Joon-Klaps
get in touch
Ask a question on Slack Open an issue on GitHub