modules/smncopynumbercaller

tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.

copy numberBAMCRAMSMN1SMN2

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

Description

tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM file

*.{bam,cram}

`bai`
`:file`

BAM/CRAM index file

*.{bai,crai}

Output

name:type

description

pattern

`smncopynumber`

`meta`
`:map`

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

`out/*.tsv`
`:file`

File containing the output of SMNCopyNumberCaller

*.{tsv}

`run_metrics`

`meta`
`:map`

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

`out/*.json`
`:file`

File containing run parameters of SMNCopyNumberCaller

*.{json}

`versions_smncopynumbercaller`

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

The name of the process

`smncopynumbercaller`
`:string`

The name of the tool

`1.1.2`
`:string`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`smncopynumbercaller`
`:string`

The name of the tool

`1.1.2`
`:string`

The expression to obtain the version of the tool

Tools

smncopynumbercaller
Apache License Version 2.0

call copy number of SMN1, SMN2, SMN2Δ7–8 from a bam file

github.com/Illumina/SMNCopyNumberCaller 10.1038/s41436-020-0754-0

modules/smncopynumbercaller

Description

Input

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

Output

`smncopynumber`

`meta`
`:map`

`out/*.tsv`
`:file`

`run_metrics`

`meta`
`:map`

`out/*.json`
`:file`

`versions_smncopynumbercaller`

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

`smncopynumbercaller`
`:string`

`1.1.2`
`:string`

Topics

`versions`

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

`smncopynumbercaller`
`:string`

`1.1.2`
`:string`

Tools

smncopynumbercaller
Apache License Version 2.0

included in

maintainer

get in touch

modules/smncopynumbercaller

Description

Input

meta:map

bam:file

bai:file

Output

smncopynumber

meta:map

out/*.tsv:file

run_metrics

meta:map

out/*.json:file

versions_smncopynumbercaller

${task.process}:string

smncopynumbercaller:string

1.1.2:string

Topics

versions

${task.process}:string

smncopynumbercaller:string

1.1.2:string

Tools

smncopynumbercaller Apache License Version 2.0

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`smncopynumber`

`meta`
`:map`

`out/*.tsv`
`:file`

`run_metrics`

`meta`
`:map`

`out/*.json`
`:file`

`versions_smncopynumbercaller`

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

`smncopynumbercaller`
`:string`

`1.1.2`
`:string`

`versions`

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

`smncopynumbercaller`
`:string`

`1.1.2`
`:string`

smncopynumbercaller
Apache License Version 2.0