Description

Sort SAM/BAM/CRAM file

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

bam{:bash}

:file

BAM/CRAM/SAM file(s)

*.{bam,cram,sam}

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘genome’ ]

fasta{:bash}

:file

Reference genome FASTA file

*.{fa,fasta,fna}

index_format{:bash}

:string

Index format to use (optional)

bai|csi|crai

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}.bam{:bash}

:file

Sorted BAM file

*.{bam}

cram{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}.cram{:bash}

:file

Sorted CRAM file

*.{cram}

sam{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}.sam{:bash}

:file

Sorted SAM file

*.{sam}

crai{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}.${extension}.crai{:bash}

:file

CRAM index file (optional)

*.crai

csi{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}.${extension}.csi{:bash}

:file

BAM index file (optional)

*.csi

bai{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

${prefix}.${extension}.bai{:bash}

:file

BAM index file (optional)

*.bai

versions_samtools{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The process the versions were collected from

samtools{:bash}

:string

The tool name

samtools version | sed '1!d;s/.* //'{:bash}

:string

The command used to generate the version of the tool

Tools

samtools
MIT

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.

http://www.htslib.org http://www.htslib.org/doc/samtools 10.1093/bioinformatics/btp352
included in
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maintainers
Github user drpatelh
Github user ewels
Github user matthdsm
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