Description

Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)

Input

name:type
description
pattern

meta

:map

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

fastx

:file

Decompressed FASTA/FASTQ input file

*.{fastq,fasta}

Output

name:type
description
pattern

fasta

meta

:map

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

${prefix}.fasta

:file

Collapsed FASTA file

*.fasta

versions_fastx

${task.process}

:string

The name of the process

fastx

:string

The name of the tool

fastx_collapser -h 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -1

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions

${task.process}

:string

The name of the process

fastx

:string

The name of the tool

fastx_collapser -h 2>&1 | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -1

:eval

The expression to obtain the version of the tool

Tools

fastx
AGPL

A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing

http://hannonlab.cshl.edu/fastx_toolkit http://hannonlab.cshl.edu/fastx_toolkit/commandline https://github.com/agordon/fastx_toolkit
maintainer
Github user jvfe
get in touch
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