modules/sentieon_datametrics

Collects multiple quality metrics from a bam file

metricsbamsentieon

https://github.com/nf-core/modules/[...]/modules/nf-core/sentieon/datametrics

Description

Collects multiple quality metrics from a bam file

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

`bai`
`:file`

Index of th sorted BAM/CRAM/SAM file

*.{bai,crai,sai}

`meta2`
`:map`

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

`fasta`
`:file`

Genome fasta file

*.{fa,fasta}

`meta3`
`:map`

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

`fai`
`:file`

Index of the genome fasta file

*.fai

`plot_results`
`:boolean`

Boolean to determine whether plots should be generated

true or false

Output

name:type

description

pattern

`mq_metrics`

`meta`
`:map`

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

`*mq_metrics.txt`
`:file`

File containing the information about mean base quality score for each sequencing cycle

*.txt

`qd_metrics`

`meta`
`:map`

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

`*qd_metrics.txt`
`:file`

File containing the information about number of bases with a specific base quality score

*.txt

`gc_summary`

`meta`
`:map`

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

`*gc_summary.txt`
`:file`

File containing the information about GC bias in the reference and the sample

*.txt

`gc_metrics`

`meta`
`:map`

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

`*gc_metrics.txt`
`:file`

File containing the information about GC bias in the reference and the sample

*.txt

`aln_metrics`

`meta`
`:map`

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

`*aln_metrics.txt`
`:file`

File containing the statistics about the alignment of the reads

*.txt

`is_metrics`

`meta`
`:map`

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

`*is_metrics.txt`
`:file`

File containing the information about statistical distribution of insert sizes

*.txt

`mq_plot`

`meta`
`:map`

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

`*mq_metrics.pdf`
`:file`

PDF containing plot of mean base quality scores

*.pdf

`qd_plot`

`meta`
`:map`

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

`*qd_metrics.pdf`
`:file`

PDF containing plot of specific base quality score

*.pdf

`is_plot`

`meta`
`:map`

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

`*is_metrics.pdf`
`:file`

PDF containing plot of insert sizes

*.pdf

`gc_plot`

`meta`
`:map`

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

`*gc_metrics.pdf`
`:file`

PDF containing plot of GC bias

*.pdf

`versions_sentieon`

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

The process the versions were collected from

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`: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

`sentieon`
`:string`

The tool name

`sentieon driver --version | sed "s/.*-//g"`
`:string`

The command used to generate the version of the tool

Tools

sentieon

Sentieon® provides complete solutions for secondary DNA/RNA analysis for a variety of sequencing platforms, including short and long reads. Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system.

sentieon.com

modules/sentieon_datametrics

Description

Input

meta:map

bam:file

bai:file

meta2:map

fasta:file

meta3:map

fai:file

plot_results:boolean

Output

mq_metrics

meta:map

*mq_metrics.txt:file

qd_metrics

meta:map

*qd_metrics.txt:file

gc_summary

meta:map

*gc_summary.txt:file

gc_metrics

meta:map

*gc_metrics.txt:file

aln_metrics

meta:map

*aln_metrics.txt:file

is_metrics

meta:map

*is_metrics.txt:file

mq_plot

meta:map

*mq_metrics.pdf:file

qd_plot

meta:map

*qd_metrics.pdf:file

is_plot

meta:map

*is_metrics.pdf:file

gc_plot

meta:map

*gc_metrics.pdf:file

versions_sentieon

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Topics

versions

${task.process}:string

sentieon:string

sentieon driver --version | sed "s/.*-//g":string

Tools

sentieon

included in

maintainer

get in touch

`meta`
`:map`

`bam`
`:file`

`bai`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`plot_results`
`:boolean`

`mq_metrics`

`meta`
`:map`

`*mq_metrics.txt`
`:file`

`qd_metrics`

`meta`
`:map`

`*qd_metrics.txt`
`:file`

`gc_summary`

`meta`
`:map`

`*gc_summary.txt`
`:file`

`gc_metrics`

`meta`
`:map`

`*gc_metrics.txt`
`:file`

`aln_metrics`

`meta`
`:map`

`*aln_metrics.txt`
`:file`

`is_metrics`

`meta`
`:map`

`*is_metrics.txt`
`:file`

`mq_plot`

`meta`
`:map`

`*mq_metrics.pdf`
`:file`

`qd_plot`

`meta`
`:map`

`*qd_metrics.pdf`
`:file`

`is_plot`

`meta`
`:map`

`*is_metrics.pdf`
`:file`

`gc_plot`

`meta`
`:map`

`*gc_metrics.pdf`
`:file`

`versions_sentieon`

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

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`

`versions`

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

`sentieon`
`:string`

`sentieon driver --version | sed "s/.*-//g"`
`:string`