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

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

Generate recalibration table and optionally perform base quality recalibration

base quality score recalibration bqsr sentieon

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @FriederikeHanssen

Maintainers: @FriederikeHanssen

Generate recalibration table and optionally perform base quality recalibration

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

include { SENTIEON_QUALCAL } from 'nf-core/sentieon/qualcal'

MIT License

Process

`Name`	`SENTIEON_QUALCAL`

Input 7 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM file from alignment `*.{bam,cram}`
`input_index` file	BAI/CRAI file from alignment `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fasta` file	The reference fasta file `*.fasta`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`fai` file	Index of reference fasta file `*.fasta.fai`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`known_sites` file	VCF files with known sites for indels / snps (optional) `*.vcf.gz`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`known_sites_tbi` file	Tabix index of the known_sites (optional) `*.vcf.gz.tbi`

#6 tuple

`meta6` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`recalibration_table` file	File containing recalibration values (optional) `*.table`

`generate_recalibrated_bams` boolean	If truem, writes recalibrated bams to disc

Output 6 channels

#1 csv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csv` file	Recalibration results output file used for plotting. (optional) `*.csv`

#2 pdf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.pdf` file	PDF file containing graphs (optional) `*.pdf`

#3 table tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.table` file	Pre Recalibration table (optional) `*.table`

#4 table_post tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.table.post` file	Post recalibration table (optional) `*.table.post`

#5 recal_alignment tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{cram,bam}` file	Recalibrated input files (optional) `*.{bam,cram}`

#6 versions_sentieon tuple


`${task.process}` string	The process the versions were collected from