Description

Creates indices of a fasta file required for alignment step

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'pEimTen1' ]

assembly (file)

Genome reference

*.{fa,fasta}

Output

Name
Description
Pattern

reference

meta (map)

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

refdata-* (file)

BAM file of mapped Hi-C sequences

refdata-*

versions_longranger

${task.process} (string)

The name of the process

longranger (string)

The name of the tool

longranger align --version | sed '1!d;s/.*(\(.*\)).*/\1/' (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

longranger (string)

The name of the tool

longranger align --version | sed '1!d;s/.*(\(.*\)).*/\1/' (eval)

The expression to obtain the version of the tool

Tools

longranger Documentation

Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.

https://github.com/10XGenomics/longrangerdoi: no DOI availableLicense: https://support.10xgenomics.com/genome-exome/software/downloads/latest
Pipelines with this module
genomeassembly
Authors