modules/picard_scatterintervalsbyns

Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases

interval_listscatterregions

https://github.com/nf-core/modules/[...]/modules/nf-core/picard/scatterintervalsbyns

Description

Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Fasta file to derive the intervals from

*.{fasta,fa,fna}

`meta2`
`:map`

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

`fai`
`:file`

Index of the fasta file

*.fai

`meta3`
`:map`

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

`dict`
`:file`

Sequence dictionary of the fasta file

*.dict

Output

name:type

description

pattern

`intervals`

`meta`
`:map`

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

`*.interval_list`
`:file`

The scattered intervals

*.interval_list

`versions_picard`

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

The process the versions were collected from

`picard`
`:string`

The tool name

`picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'`
`: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

`picard`
`:string`

The tool name

`picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'`
`:string`

The command used to generate the version of the tool

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

broadinstitute.github.io/picard https://github.com/broadinstitute/picard

modules/picard_scatterintervalsbyns

Description

Input

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`fai`
`:file`

`meta3`
`:map`

`dict`
`:file`

Output

`intervals`

`meta`
`:map`

`*.interval_list`
`:file`

`versions_picard`

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

`picard`
`:string`

`picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'`
`:string`

Topics

`versions`

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

`picard`
`:string`

`picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'`
`:string`

Tools

picard
MIT

maintainer

get in touch

modules/picard_scatterintervalsbyns

Description

Input

meta:map

fasta:file

meta2:map

fai:file

meta3:map

dict:file

Output

intervals

meta:map

*.interval_list:file

versions_picard

${task.process}:string

picard:string

picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p':string

Topics

versions

${task.process}:string

picard:string

picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p':string

Tools

picard MIT

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`fai`
`:file`

`meta3`
`:map`

`dict`
`:file`

`intervals`

`meta`
`:map`

`*.interval_list`
`:file`

`versions_picard`

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

`picard`
`:string`

`picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'`
`:string`

`versions`

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

`picard`
`:string`

`picard ScatterIntervalsByNs --version 2>&1 | sed -n 's/.*Version://p'`
`:string`

picard
MIT