Nextflow Registry | nf-core/dragmap/align@0.0.0-6c4ed3a

nf-core/dragmap/align @ 0.0.0-6c4ed3a

Performs fastq alignment to a reference using DRAGMAP

alignment map fastq bam sam

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @edmundmiller

Maintainers: @edmundmiller

Performs fastq alignment to a reference using DRAGMAP

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

include { DRAGMAP_ALIGN } from 'nf-core/dragmap/align'

MIT License

Process

`Name`	`DRAGMAP_ALIGN`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test', single_end:false ]
`hashmap` file	DRAGMAP hash table `Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}`

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. [ id:'genome']
`fasta` file	Genome fasta reference files `*.{fa,fasta,fna}`

`sort_bam` boolean	Sort the BAM file

Output 9 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.bam` file	Output BAM file containing read alignments `*.{bam}`

#2 csi tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.csi` file	Index file for CRAM file `*.{csi}`

#3 log tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	Log file `*.{log}`

#4 sam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.sam` file	Output SAM file containing read alignments `*.{sam}`

#5 crai tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.crai` file	Index file for CRAM file `*.{crai}`

#6 cram tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.cram` file	Output CRAM file containing read alignments `*.{cram}`

#7 versions_pigz tuple

`${task.process}` string	The name of the process
`pigz` string	The name of the tool
`pigz --version 2>&1 \| sed 's/pigz //'` eval	The expression to obtain the version of the tool

#8 versions_dragmap tuple

`${task.process}` string	The name of the process
`dragmap` string	The name of the tool
`dragen-os --version 2>&1` eval	The expression to obtain the version of the tool

#9 versions_samtools tuple

`${task.process}` string