modules/samtools_sort

Sort SAM/BAM/CRAM file

sortbamsamcram

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

Description

Sort SAM/BAM/CRAM file

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM/SAM file(s)

*.{bam,cram,sam}

`meta2`
`:map`

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

`fasta`
`:file`

Reference genome FASTA file

*.{fa,fasta,fna}

`index_format`
`:string`

Index format to use (optional)

bai|csi|crai

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`${prefix}.bam`
`:file`

Sorted BAM file

*.{bam}

`cram`

`meta`
`:map`

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

`${prefix}.cram`
`:file`

Sorted CRAM file

*.{cram}

`sam`

`meta`
`:map`

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

`${prefix}.sam`
`:file`

Sorted SAM file

*.{sam}

`crai`

`meta`
`:map`

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

`${prefix}.${extension}.crai`
`:file`

CRAM index file (optional)

*.crai

`csi`

`meta`
`:map`

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

`${prefix}.${extension}.csi`
`:file`

BAM index file (optional)

*.csi

`bai`

`meta`
`:map`

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

`${prefix}.${extension}.bai`
`:file`

BAM index file (optional)

*.bai

`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_sort

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index_format`
`:string`

Output

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`cram`

`meta`
`:map`

`${prefix}.cram`
`:file`

`sam`

`meta`
`:map`

`${prefix}.sam`
`:file`

`crai`

`meta`
`:map`

`${prefix}.${extension}.crai`
`:file`

`csi`

`meta`
`:map`

`${prefix}.${extension}.csi`
`:file`

`bai`

`meta`
`:map`

`${prefix}.${extension}.bai`
`:file`

`versions`

`versions.yml`
`:file`

Tools

samtools
MIT

included in

maintainers

get in touch

modules/samtools_sort

Description

Input

meta:map

bam:file

meta2:map

fasta:file

index_format:string

Output

bam

meta:map

${prefix}.bam:file

cram

meta:map

${prefix}.cram:file

sam

meta:map

${prefix}.sam:file

crai

meta:map

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

csi

meta:map

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

bai

meta:map

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

versions

versions.yml:file

Tools

samtools MIT

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index_format`
`:string`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`cram`

`meta`
`:map`

`${prefix}.cram`
`:file`

`sam`

`meta`
`:map`

`${prefix}.sam`
`:file`

`crai`

`meta`
`:map`

`${prefix}.${extension}.crai`
`:file`

`csi`

`meta`
`:map`

`${prefix}.${extension}.csi`
`:file`

`bai`

`meta`
`:map`

`${prefix}.${extension}.bai`
`:file`

`versions`

`versions.yml`
`:file`

samtools
MIT