Description

convert and then index CRAM -> BAM or 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

BAM/CRAM file

*.{bam,cram}

index{:bash}

:file

BAM/CRAM index file

*.{bai,crai}

meta2{:bash}

:map

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

fasta{:bash}

:file

Reference file to create the CRAM file

*.{fasta,fa}

fai{:bash}

:file

Reference index file to create the CRAM file

*.{fai}

Output

name:type
description
pattern

bam{:bash}

meta{:bash}

:map

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

*.bam{:bash}

:file

filtered/converted BAM file

*{.bam}

cram{:bash}

meta{:bash}

:map

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

*.cram{:bash}

:file

filtered/converted CRAM file

*{cram}

bai{:bash}

meta{:bash}

:map

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

*.bai{:bash}

:file

filtered/converted BAM index

*{.bai}

crai{:bash}

meta{:bash}

:map

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

*.crai{:bash}

:file

filtered/converted CRAM index

*{.crai}

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
dropgenomicrelatednessrnadnavarrnavarsarek
maintainers
Github user FriederikeHanssen
Github user maxulysse
Github user matthdsm
get in touch
Ask a question on Slack Open an issue on GitHub