Nextflow Registry | nf-core/samtools/sormadup@0.0.0-0c7146d

nf-core/samtools/sormadup @ 0.0.0-0c7146d

Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file

cat collate fixmate sort markduplicates bam sam cram multi-tool

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @matthdsm

Maintainers: @matthdsm

Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file

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

include { SAMTOOLS_SORMADUP } from 'nf-core/samtools/sormadup'

MIT License

Process

`Name`	`SAMTOOLS_SORMADUP`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`input` file	BAM/CRAM/SAM files `*.{bam,cram,sam}`

#2 tuple

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

Output 6 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	Sorted and duplicate marked BAM file `*.bam`

#2 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csi` file	Sorted and duplicate marked BAM index file `*.csi`

#3 crai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.crai` file	Sorted and duplicate marked CRAM index file `*.crai`

#4 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	Sorted and duplicate marked CRAM file `*.cram`

#5 metrics tuple

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

#6 versions_samtools tuple

`${task.process}` string	The process the versions were collected from
`samtools` string	The tool name
`samtools version \| sed '1!d;s/.* //'` eval	The command used to generate the version of the tool

Tool	Description	Homepage
samtools_cat	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/
samtools_collate	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/
samtools_fixmate	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/
samtools_sort	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/
samtools_markdup	SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA.	http://www.htslib.org/