modules/samtools_index

Index SAM/BAM/CRAM file

indexbamsamcram

https://github.com/nf-core/modules/[...]/modules/nf-core/samtools/index

Description

Index SAM/BAM/CRAM file

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

input file

Output

name:type

description

pattern

`bai`

`meta`
`:map`

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

`*.bai`
`:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`csi`

`meta`
`:map`

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

`*.csi`
`:file`

CSI index file

*.{csi}

`crai`

`meta`
`:map`

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

`*.crai`
`:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`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

modules/samtools_index

Description

Input

`meta`
`:map`

`input`
`:file`

Output

`bai`

`meta`
`:map`

`*.bai`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`crai`

`meta`
`:map`

`*.crai`
`:file`

`versions`

`versions.yml`
`:file`

Tools

samtools
MIT

included in

maintainers

get in touch

modules/samtools_index

Description

Input

meta:map

input:file

Output

bai

meta:map

*.bai:file

csi

meta:map

*.csi:file

crai

meta:map

*.crai:file

versions

versions.yml:file

Tools

samtools MIT

included in

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`csi`

`meta`
`:map`

`*.csi`
`:file`

`crai`

`meta`
`:map`

`*.crai`
`:file`

`versions`

`versions.yml`
`:file`

samtools
MIT