modules/parabricks_fq2bammeth

NVIDIA Clara Parabricks GPU-accelerated fast, accurate algorithm for mapping methylated DNA sequence reads to a reference genome, performing local alignment, and producing alignment for different parts of the query sequence

alignsortbqsrduplicatesbwameth

https://github.com/nf-core/modules/[...]/modules/nf-core/parabricks/fq2bammeth

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`reads`
`:file`

fastq.gz files

*.fastq.gz

`meta2`
`:map`

Groovy Map containing fasta information

`fasta`
`:file`

reference fasta file - must be unzipped

*.fasta

`meta3`
`:map`

Groovy Map containing index information

`index`
`:file`

reference BWA index

*.{amb,ann,bwt,pac,sa}

`known_sites`
`:file`

(optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR.

*.vcf.gz

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Sorted BAM file

*.bam

`bai`

`meta`
`:map`

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

`*.bai`
`:file`

index corresponding to sorted BAM file

*.bai

`qc_metrics`

`qc_metrics`
`:directory`

(optional) optional directory of qc metrics

qc_metrics

`bqsr_table`

`*.table`
`:file`

(optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr

*.table

`duplicate_metrics`

`duplicate-metrics.txt`
`:file`

(optional) metrics calculated from marking duplicates in the bam file

*-duplicate-metrics.txt

`versions_parabricks`

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

The process the versions were collected from

`parabricks`
`:string`

The tool name

`pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'`
`:string`

The command used to generate the version of the tool

Topics

name:type

description

pattern

`versions`

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

The process the versions were collected from

`parabricks`
`:string`

The tool name

`pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'`
`:string`

The command used to generate the version of the tool

Tools

parabricks
custom

NVIDIA Clara Parabricks GPU-accelerated genomics tools

nvidia.com/en-us/clara/genomics docs.nvidia.com/clara/parabricks/latest

modules/parabricks_fq2bammeth

Description

Input

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`index`
`:file`

`known_sites`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`qc_metrics`

`qc_metrics`
`:directory`

`bqsr_table`

`*.table`
`:file`

`duplicate_metrics`

`duplicate-metrics.txt`
`:file`

`versions_parabricks`

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

`parabricks`
`:string`

`pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'`
`:string`

Topics

`versions`

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

`parabricks`
`:string`

`pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'`
`:string`

Tools

parabricks
custom

included in

maintainers

get in touch

modules/parabricks_fq2bammeth

Description

Input

meta:map

reads:file

meta2:map

fasta:file

meta3:map

index:file

known_sites:file

Output

bam

meta:map

*.bam:file

bai

meta:map

*.bai:file

qc_metrics

qc_metrics:directory

bqsr_table

*.table:file

duplicate_metrics

duplicate-metrics.txt:file

versions_parabricks

${task.process}:string

parabricks:string

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//':string

Topics

versions

${task.process}:string

parabricks:string

pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//':string

Tools

parabricks custom

included in

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`index`
`:file`

`known_sites`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bai`

`meta`
`:map`

`*.bai`
`:file`

`qc_metrics`

`qc_metrics`
`:directory`

`bqsr_table`

`*.table`
`:file`

`duplicate_metrics`

`duplicate-metrics.txt`
`:file`

`versions_parabricks`

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

`parabricks`
`:string`

`pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'`
`:string`

`versions`

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

`parabricks`
`:string`

`pbrun version | grep -m1 '^pbrun:' | sed 's/^pbrun:[[:space:]]*//'`
`:string`

parabricks
custom