Description

Index SAM/BAM/CRAM file

Input

name:type
description
pattern

meta{:bash}

:map

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

input{:bash}

:file

input file

Output

name:type
description
pattern

bai{:bash}

meta{:bash}

:map

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

*.bai{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

csi{:bash}

meta{:bash}

:map

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

*.csi{:bash}

:file

CSI index file

*.{csi}

crai{:bash}

meta{:bash}

:map

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

*.crai{:bash}

:file

BAM/CRAM/SAM index file

*.{bai,crai,sai}

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

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

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

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

:eval

The expression to obtain 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
alleleexpressionatacseqbacassbamtofastqcallingcardschipseqcircdnacircrnacoproidcreatepanelrefscrisprseqcutandrundropevexplorergenomeassemblergenomicrelatednesshgtseqhicarlncpipemagmagmapmetatdenovomethylongmethylseqnanoseqnascentpacsomaticpacvarpathogensurveillancephageannotatorphaseimputeradseqrarediseasereadsimulatorriboseqrnadnavarrnafusionrnaseqrnasplicernavarsammyseqsarekscnanoseqseqinspectorsmrnaseqssdstaxprofilertbanalyzervariantcatalogueviralintegrationviralmetagenomeviralrecon
maintainers
Github user drpatelh
Github user ewels
Github user maxulysse
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