Description

Performs alignment of Illumina 10X sequencing data to a Longranger indexed reference genome.

Does not have a container configured - a pipeline using this module must supply one via the config file. The container defined in the module test is accessible interally to Sanger users only and will need to be changed if outside users wish to test the module.

Input

Name
Description
Pattern

meta (map)

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

fastq (file)

Illumina 10X Fastq files

*.fastq.gz

meta2 (map)

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

reference (file)

Longranger reference from longranger/mkref

Output

Name
Description
Pattern

bai

meta (map)

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

${prefix}/outs/possorted_bam.bam.bai (file)

BAM file index

bam

meta (map)

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

${prefix}/outs/possorted_bam.bam (file)

Sorted BAM file of 10X reads mapped to the reference

csv

meta (map)

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

${prefix}/outs/summary.csv (file)

Summary CSV describing Longranger process

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