Description

convert and then index CRAM -> BAM or BAM -> CRAM file

Input

name:type
description
pattern

meta:map

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

]

input:file

BAM/CRAM file

*.{bam,cram}

index:file

BAM/CRAM index file

*.{bai,crai}

meta2:map

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

]

fasta:file

Reference file to create the CRAM file

*.{fasta,fa}

meta3:map

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

]

fai:file

Reference index file to create the CRAM file

*.{fai}

Output

name:type
description
pattern

bam

meta:map

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

]

*.bam:file

filtered/converted BAM file

*{.bam}

cram

meta:map

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

]

*.cram:file

filtered/converted CRAM file

*{cram}

bai

meta:map

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

]

*.bai:file

filtered/converted BAM index

*{.bai}

crai

meta:map

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

]

*.crai:file

filtered/converted CRAM index

*{.crai}

versions

versions.yml:file

File containing software versions

versions.yml

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