modules/samtools_fixmate

Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.

fixmatesamtoolsinsert sizerepairbampairedread pairs

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

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`input`
`:file`

BAM/CRAM/SAM file, must be sorted by name, not coordinate

*.{bam,cram,sam}

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

*.{bam}

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

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

*.{bam}

`cram`

`meta`
`:map`

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

*.{bam}

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

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

*.{cram}

`sam`

`meta`
`:map`

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

*.{bam}

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

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

*.{sam}

`versions_samtools`

`${task.process}`
`:string`

The process the versions were collected from

`samtools`
`:string`

The tool name

`samtools version | sed '1!d;s/.* //'`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The process the versions were collected from

`samtools`
`:string`

The tool name

`samtools version | sed '1!d;s/.* //'`
`:string`

The command used to generate 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 https://github.com/samtools/samtools 10.1093/bioinformatics/btp352

modules/samtools_fixmate

Description

Input

`meta`
`:map`

`input`
`:file`

Output

`bam`

`meta`
`:map`

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

`cram`

`meta`
`:map`

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

`sam`

`meta`
`:map`

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

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:string`

Topics

`versions`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:string`

Tools

samtools
MIT

maintainers

get in touch

modules/samtools_fixmate

Description

Input

meta:map

input:file

Output

bam

meta:map

${prefix}.bam:map

cram

meta:map

${prefix}.cram:map

sam

meta:map

${prefix}.sam:map

versions_samtools

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':string

Topics

versions

${task.process}:string

samtools:string

samtools version | sed '1!d;s/.* //':string

Tools

samtools MIT

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`bam`

`meta`
`:map`

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

`cram`

`meta`
`:map`

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

`sam`

`meta`
`:map`

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

`versions_samtools`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:string`

`versions`

`${task.process}`
`:string`

`samtools`
`:string`

`samtools version | sed '1!d;s/.* //'`
`:string`

samtools
MIT