Nextflow Registry | nf-core/mapad/map@0.0.0-0c7146d

nf-core/mapad/map @ 0.0.0-0c7146d

Map short-reads to an indexed reference genome

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jch-13

Maintainers: @jch-13

Map short-reads to an indexed reference genome

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

include { MAPAD_MAP } from 'nf-core/mapad/map'

MIT License

Process

`Name`	`MAPAD_MAP`

Input 9 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory) `*.{bam,cram,fastq,fastq.gz,fq,fq.gz}`

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. [ id:'test', single_end:false ]
`index` file	mapAD genome index files (mandatory) `*.{tbw,tle,toc,tos,tpi,trt,tsa}`

`mismatch_parameter` float	Minimum probability of the number of mismatches under `-D` base error rate

`double_stranded_library` boolean	Library preparation method - specify if double stranded else it's assumed single stranded

`five_prime_overhang` float	5'-overhang length parameter

`three_prime_overhang` float	3'-overhang length parameter

`deam_rate_double_stranded` float	Deamination rate in double-stranded stem of a read

`deam_rate_single_stranded` float	Deamination rate in single-stranded ends of a read

`indel_rate` float	Expected rate of indels between reads and reference

Output 2 channels

#1 bam tuple

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

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

Tool	Description	Homepage
mapad	An aDNA aware short-read mapper	https://github.com/mpieva/mapAD

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:53:59 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fmapad%2Fmap/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/mapad/map/blobs/sha256:e9f48305c80b62a2494e501a98f094d61e48dafc25c7988b63502f157d6e6d8e
Size	2.8 KB
Checksum	sha256:e9f48305c80b62a2494e501a98f094d61e48dafc25c7988b63502f157d6e6d8e
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d