Description

Aligns a subset of Hi-C reads from a CRAM file to a reference genome using bwa-mem2, pipes the resulting alignments through samtools fixmate and samtools sort, outputting an alignment in BAM format.

Input

Name
Description
Pattern

meta (map)

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

cram (file)

CRAM file containing Hi-C sequences to align

*.cram

crai (file)

CRAM index file

*.crai

rglines (list)

A list of strings, each a valid SAM-format @RG header line, to pass to the aligner

meta2 (map)

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

index (file)

bwa-mem2 index of the reference to be aligned to

reference (file)

FASTA file containing reference for alignment

*.fasta(.gz)?

chunkn (integer)

Integer index of CRAM chunk to map

range (list)

Start and end indices defining CRAM slices to align

Output

Name
Description
Pattern

bam

meta (map)

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

*.bam (file)

BAM file of mapped Hi-C sequences

*.bam

versions_bwamem2

${task.process} (string)

Name of the process

bwamem2 (string)

The name of the tool

bwa-mem2 version 2>&1 | grep -o -E "[0-9]+(\.[0-9]+)+" (eval)

The expression to obtain the version of the tool

versions_samtools

${task.process} (string)

Name of the process

samtools (string)

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //" (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

Name of the process

bwamem2 (string)

The name of the tool

bwa-mem2 version 2>&1 | grep -o -E "[0-9]+(\.[0-9]+)+" (eval)

The expression to obtain the version of the tool

${task.process} (string)

Name of the process

samtools (string)

Name of the tool

samtools --version | head -1 | sed -e "s/samtools //" (eval)

The expression to obtain the version of the tool

Tools

samtools Documentation

SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.

doi: 10.1093/bioinformatics/btp352License: MIT

bwa Documentation

BWA-mem2 is a software package for mapping DNA sequences against a large reference genome, such as the human genome.

License: MIT
Pipelines with this module
genomeassemblymetagenomeassembly
Authors