modules/gatk4_calibratedragstrmodel

estimates the parameters for the DRAGstr model

gatk4bamcramsamcalibratedragstrmodel

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

Description

estimates the parameters for the DRAGstr model

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM/CRAM/SAM file

*.{bam,cram,sam}

`bam_index`
`:file`

index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

`fasta`
`:file`

The reference FASTA file

*.{fasta,fa}

`fasta_fai`
`:file`

The index of the reference FASTA file

*.fai

`dict`
`:file`

The sequence dictionary of the reference FASTA file

*.dict

`strtablefile`
`:file`

The StrTableFile zip folder of the reference FASTA file

*.zip

Output

name:type

description

pattern

`dragstr_model`

`meta`
`:map`

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

`*.txt`
`:file`

The DragSTR model

*.txt

`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/360057441571-CalibrateDragstrModel-BETA- https://github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590

modules/gatk4_calibratedragstrmodel

Description

Input

`meta`
`:map`

`bam`
`:file`

`bam_index`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`dict`
`:file`

`strtablefile`
`:file`

Output

`dragstr_model`

`meta`
`:map`

`*.txt`
`: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

maintainer

get in touch

modules/gatk4_calibratedragstrmodel

Description

Input

meta:map

bam:file

bam_index:file

fasta:file

fasta_fai:file

dict:file

strtablefile:file

Output

dragstr_model

meta:map

*.txt: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

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bam_index`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`dict`
`:file`

`strtablefile`
`:file`

`dragstr_model`

`meta`
`:map`

`*.txt`
`: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