Nextflow Registry | nf-core/pbcpgtools/alignedbamtocpgscores@0.0.0-6c4ed3a

nf-core/pbcpgtools/alignedbamtocpgscores @ 0.0.0-6c4ed3a

Converts aligned BAM files into CpG methylation scores

methylation cpg pacbio

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @inemesb

Maintainers: @inemesb

Converts aligned BAM files into CpG methylation scores

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

include { PBCPGTOOLS_ALIGNEDBAMTOCPGSCORES } from 'nf-core/pbcpgtools/alignedbamtocpgscores'

MIT License

Process

`Name`	`PBCPGTOOLS_ALIGNEDBAMTOCPGSCORES`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`bam` file	BAM/CRAM file `*.{bam,cram}`
`bai` file	Index of BAM/CRAM file `*.{bai,crai,csi}`

Output 10 channels

#1 hap1_bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.hap1.bed.gz` file	Zipped BED file with CpG methylation scores for haplotype 1 `*.{hap1.bed.gz}`

#2 hap2_bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.hap2.bed.gz` file	Zipped BED file with CpG methylation scores for haplotype 2 `*.{hap2.bed.gz}`

#3 hap1_bigwig tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.hap1.bw` file	Bigwig file for visualization in IGV `*.{hap1.bw}`

#4 hap2_bigwig tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.hap2.bw` file	Bigwig file for visualization in IGV `*.{hap2.bw}`

#5 combined_bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.combined.bed.gz` file	Zipped BED file with CpG methylation scores for both haplotypes `*.{combined.bed.gz}`

#6 hap1_bed_index tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.hap1.bed.gz.tbi` file	Index of hap1 zipped BED file `*.{hap1.bed.gz.tbi}`

#7 hap2_bed_index tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.hap2.bed.gz.tbi` file	Index of hap2 zipped BED file `*.{hap2.bed.gz.tbi}`

#8 combined_bigwig tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.combined.bw` file	Bigwig file for visualization in IGV `*.{combined.bw}`

#9 combined_bed_index tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`*.combined.bed.gz.tbi` file	Index of combined zipped BED file `*.{combined.bed.gz.tbi}`

#10 versions_pbcpgtools tuple

`${task.process}` string	The name of the process
`pbcpgtools` string	The name of the tool
`aligned_bam_to_cpg_scores --version \| sed 's/.* //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
pbcpgtools	Collection of tools for the analysis of CpG data	https://github.com/PacificBiosciences/pb-CpG-tools