modules/fgbio_filterconsensusreads

Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.

fgbiofilterconsensusumiduplexumi

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

Description

Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads.

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

BAM file

*.bam

`meta2`
`:map`

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

`fasta`
`:file`

Fasta file containing genomic sequence information

*.{fa,fasta,fna}

`index`
`:file`

Fasta index file

*.fai

`dict`
`:file`

Fasta dictionary file

*.dict

`min_reads`
`:integer`

Minimum number of reads required to keep a consensus read

`min_baseq`
`:file`

Minimum base quality to consider

`max_base_error_rate`
`:file`

Maximum base error rate for a position before it is replaced with an N.

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`${prefix}.bam`
`:file`

Filtered consensus BAM file

*.bam

`versions_fgbio`

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

The process the versions were collected from

`fgbio`
`:string`

The tool name

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`fgbio`
`:string`

The tool name

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

The expression to obtain the version of the tool

Tools

fgbio
MIT

A set of tools for working with genomic and high throughput sequencing data, including UMIs

http://fulcrumgenomics.github.io/fgbio http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads https://github.com/fulcrumgenomics/fgbio

modules/fgbio_filterconsensusreads

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index`
`:file`

`dict`
`:file`

`min_reads`
`:integer`

`min_baseq`
`:file`

`max_base_error_rate`
`:file`

Output

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`versions_fgbio`

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

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

Topics

`versions`

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

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

Tools

fgbio
MIT

included in

maintainer

get in touch

modules/fgbio_filterconsensusreads

Description

Input

meta:map

bam:file

meta2:map

fasta:file

index:file

dict:file

min_reads:integer

min_baseq:file

max_base_error_rate:file

Output

bam

meta:map

${prefix}.bam:file

versions_fgbio

${task.process}:string

fgbio:string

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//":eval

Topics

versions

${task.process}:string

fgbio:string

fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//":eval

Tools

fgbio MIT

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index`
`:file`

`dict`
`:file`

`min_reads`
`:integer`

`min_baseq`
`:file`

`max_base_error_rate`
`:file`

`bam`

`meta`
`:map`

`${prefix}.bam`
`:file`

`versions_fgbio`

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

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

`versions`

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

`fgbio`
`:string`

`fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.Version: //;s/\[.$//"`
`:eval`

fgbio
MIT