Nextflow Registry | nf-core/samtools/view@0.0.0-6c4ed3a

nf-core/samtools/view @ 0.0.0-6c4ed3a

filter/convert SAM/BAM/CRAM file

view bam sam cram

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @drpatelh @joseespinosa @FriederikeHanssen @priyanka-surana

Maintainers: @drpatelh @joseespinosa @FriederikeHanssen @priyanka-surana @matthdsm

filter/convert SAM/BAM/CRAM file

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

include { SAMTOOLS_VIEW } from 'nf-core/samtools/view'

MIT License

Process

`Name`	`SAMTOOLS_VIEW`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM file `*.{bam,cram,sam}`
`index` file	BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) `*.{.bai,.csi,.crai}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'genome' ]
`fasta` file	Fasta reference file `*.{fasta,fa}`
`fai` file	Fasta reference file index `*.{fai}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`qname` file	Optional file with read names to output only select alignments `*.{txt,list}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bed` file	Optional BED file for filtering alignments by genomic region (-L) `*.{bed}`

`index_format` string	Index format, used together with ext.args = '--write-index' `bai\|csi\|crai`

Output 9 channels

#1 bai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.${file_type}.bai` file	optional BAM file index `*.{bai}`

#2 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.bam` file	optional filtered/converted BAM file `*.{bam}`

#3 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.${file_type}.csi` file	optional tabix BAM file index `*.{csi}`

#4 sam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.sam` file	optional filtered/converted SAM file `*.{sam}`

#5 crai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.${file_type}.crai` file	optional CRAM file index `*.{crai}`

#6 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.cram` file	optional filtered/converted CRAM file `*.{cram}`

#7 unselected tuple

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