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 ]

umis (file)

Fastq file(s) containing UMIs

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

Output

Name (Type)
Description
Pattern

meta (map)

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

dedup (file)

Deduplicated Fastq file(s)

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

annotated (file)

Annotated Fastq file(s)

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

stats (directory)

Directory containg statistics file, use for multiqc.

${prefix}/

log (file)

Log file of humid, containing progress and errors

*.log

versions (file)

File containing software versions

versions.yml
maintainer
Github user Joon-Klaps
get in touch
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