modules/gatk4_collectreadcounts

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.

collectreadcountsbamcramgatk4

https://github.com/nf-core/modules/[...]/modules/nf-core/gatk4/collectreadcounts

Description

Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.

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}

`input_index`
`:file`

BAM/CRAM/SAM index file

*.{bai,crai,sai}

`intervals`
`:file`

A file containing the specified intervals

*.{bed,intervals}

`meta2`
`:map`

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

`fasta`
`:file`

Optional - Reference FASTA

*.{fasta,fa}

`meta3`
`:map`

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

`fai`
`:file`

Optional - Index of the reference FASTA file

*.fai

`meta4`
`:map`

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

`dict`
`:file`

Optional - Sequence dictionary of the reference FASTA file

*.dict

Output

name:type

description

pattern

`hdf5`

`meta`
`:map`

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

`*.hdf5`
`:file`

The read counts in hdf5 format

*.hdf5

`tsv`

`meta`
`:map`

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

`*.tsv`
`:file`

The read counts in TSV format

*.tsv

`versions_gatk4`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gatk4`
`:string`

The name of the tool

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gatk4
Apache-2.0

Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_collectreadcounts

Description

Input

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

Output

`hdf5`

`meta`
`:map`

`*.hdf5`
`:file`

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Topics

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

Tools

gatk4
Apache-2.0

included in

maintainer

get in touch

modules/gatk4_collectreadcounts

Description

Input

meta:map

input:file

input_index:file

intervals:file

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

dict:file

Output

hdf5

meta:map

*.hdf5:file

tsv

meta:map

*.tsv:file

versions_gatk4

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Topics

versions

${task.process}:string

gatk4:string

gatk --version | sed -n '/GATK.*v/s/.*v//p':eval

Tools

gatk4 Apache-2.0

included in

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`intervals`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`dict`
`:file`

`hdf5`

`meta`
`:map`

`*.hdf5`
`:file`

`tsv`

`meta`
`:map`

`*.tsv`
`:file`

`versions_gatk4`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

`versions`

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

`gatk4`
`:string`

`gatk --version | sed -n '/GATK.v/s/.v//p'`
`:eval`

gatk4
Apache-2.0