modules/samtools_splitheader

Extract header lines from a SAM/BAM/CRAM file into separate files depending on type

viewbamsamcramreadgroupprogramsequenceheader

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

Description

Extract header lines from a SAM/BAM/CRAM file into separate files depending on type

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

*.{bam,cram,sam}

Output

name:type

description

pattern

`readgroup`

`meta`
`:map`

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

`*_readgroups.txt`
`:file`

Text file containing read group (@RG) lines from SAM header

`programs`

`meta`
`:map`

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

`*_programs.txt`
`:file`

Text file containing program (@PG) lines from SAM header

`sequences`

`meta`
`:map`

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

`*_sequences.txt`
`:file`

Text file containing sequence (@SQ) lines from SAM header

`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 10.1093/bioinformatics/btp352

modules/samtools_splitheader

Description

Input

`meta`
`:map`

`input`
`:file`

Output

`readgroup`

`meta`
`:map`

`*_readgroups.txt`
`:file`

`programs`

`meta`
`:map`

`*_programs.txt`
`:file`

`sequences`

`meta`
`:map`

`*_sequences.txt`
`:file`

`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_splitheader

Description

Input

meta :map

input :file

Output

readgroup

meta :map

*_readgroups.txt :file

programs

meta :map

*_programs.txt :file

sequences

meta :map

*_sequences.txt :file

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

samtoolsMIT

maintainers

get in touch

`meta`
`:map`

`input`
`:file`

`readgroup`

`meta`
`:map`

`*_readgroups.txt`
`:file`

`programs`

`meta`
`:map`

`*_programs.txt`
`:file`

`sequences`

`meta`
`:map`

`*_sequences.txt`
`:file`

`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