Nextflow Registry | nf-core/sentieon/datametrics@0.0.0-6c4ed3a

nf-core/sentieon/datametrics @ 0.0.0-6c4ed3a

Collects multiple quality metrics from a bam file

metrics bam sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @ramprasadn

Maintainers: @ramprasadn

Collects multiple quality metrics from a bam file

Add the following snippet to your workflow script to include this module.

include { SENTIEON_DATAMETRICS } from 'nf-core/sentieon/datametrics'

MIT License

Process

`Name`	`SENTIEON_DATAMETRICS`

Input 4 channels

#1 tuple

`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}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`fasta` file	Genome fasta file `*.{fa,fasta}`

#3 tuple

`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 11 channels

#1 gc_plot tuple

`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`

#2 is_plot tuple

`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`

#3 mq_plot tuple

`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`

#4 qd_plot tuple

`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`

#5 gc_metrics tuple

`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`

#6 gc_summary tuple

`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`

#7 is_metrics tuple

`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`

#8 mq_metrics tuple

`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`

#9 qd_metrics tuple

`meta` map	Groovy Map containing samp