modules/gatk4_collectsvevidence

Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping.

gatk4collectsvevidencestructural variantsmetrics

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

Description

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`

Index of the BAM/CRAM/SAM file

*.{bai,crai,sai}

`site_depth_vcf`
`:file`

Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output

*.vcf.gz

`site_depth_vcf_tbi`
`:file`

Optional - input VCF TBI of SNPs marking loci for site depths, needed for the site depths output

*.vcf.gz.tbi

`fasta`
`:file`

Optional - reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

`fasta_fai`
`:file`

Optional - index of the reference FASTA file needed when the input is a CRAM file

*.fai

`dict`
`:file`

Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.dict

Output

name:type

description

pattern

`split_read_evidence`

`meta`
`:map`

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

`*.sr.txt.gz`
`:file`

Output file for split read evidence

*.sr.txt.gz

`split_read_evidence_index`

`meta`
`:map`

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

`*.sr.txt.gz.tbi`
`:file`

Index of the output file for split read evidence

*.sr.txt.gz.tbi

`paired_end_evidence`

`meta`
`:map`

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

`*.pe.txt.gz`
`:file`

Output file for paired end evidence

*.pe.txt.gz

`paired_end_evidence_index`

`meta`
`:map`

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

`*.pe.txt.gz.tbi`
`:file`

Index of the output file for paired end evidence

*.pe.txt.gz.tbi

`site_depths`

`meta`
`:map`

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

`*.sd.txt.gz`
`:file`

Output file for site depths

*.sd.txt.gz

`site_depths_index`

`meta`
`:map`

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

`*.sd.txt.gz.tbi`
`:file`

Index of the output file for site depths

*.sd.txt.gz.tbi

`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
BSD-3-clause

Genome Analysis Toolkit (GATK4)

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

modules/gatk4_collectsvevidence

Description

Input

meta:map

input:file

input_index:file

site_depth_vcf:file

site_depth_vcf_tbi:file

fasta:file

fasta_fai:file

dict:file

Output

split_read_evidence

meta:map

*.sr.txt.gz:file

split_read_evidence_index

meta:map

*.sr.txt.gz.tbi:file

paired_end_evidence

meta:map

*.pe.txt.gz:file

paired_end_evidence_index

meta:map

*.pe.txt.gz.tbi:file

site_depths

meta:map

*.sd.txt.gz:file

site_depths_index

meta:map

*.sd.txt.gz.tbi: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 BSD-3-clause

maintainer

get in touch

`meta`
`:map`

`input`
`:file`

`input_index`
`:file`

`site_depth_vcf`
`:file`

`site_depth_vcf_tbi`
`:file`

`fasta`
`:file`

`fasta_fai`
`:file`

`dict`
`:file`

`split_read_evidence`

`meta`
`:map`

`*.sr.txt.gz`
`:file`

`split_read_evidence_index`

`meta`
`:map`

`*.sr.txt.gz.tbi`
`:file`

`paired_end_evidence`

`meta`
`:map`

`*.pe.txt.gz`
`:file`

`paired_end_evidence_index`

`meta`
`:map`

`*.pe.txt.gz.tbi`
`:file`

`site_depths`

`meta`
`:map`

`*.sd.txt.gz`
`:file`

`site_depths_index`

`meta`
`:map`

`*.sd.txt.gz.tbi`
`: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
BSD-3-clause