Nextflow Registry | nf-core/circularmapper/realignsamfile@0.0.0-0c7146d

nf-core/circularmapper/realignsamfile @ 0.0.0-0c7146d

Realign reads mapped with BWA to elongated reference genome

realign circular map reference fasta bam short-read bwa

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @shyama-mama @jbv2 @TCLamnidis

Realign reads mapped with BWA to elongated reference genome

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

include { CIRCULARMAPPER_REALIGNSAMFILE } from 'nf-core/circularmapper/realignsamfile'

MIT License

Process

`Name`	`CIRCULARMAPPER_REALIGNSAMFILE`

Input 4 channels

#1 tuple

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

#2 tuple

`meta2` map	Groovy Map containing reference information e.g. `[ id:'test' ]`
`fasta` file	Input elongated genome fasta

#3 tuple

`meta3` map	Groovy Map containing reference information e.g. `[ id:'test' ]`
`elongation_factor` integer	The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by

#4 tuple

`meta4` map	Groovy Map containing reference information e.g. `[ id:'test' ]`
`elongated_chr_list` file	File listing the chromosomes that were elongated `*_elongated`

Output 2 channels

#1 bam tuple

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

#2 versions_circularmapper tuple

`${task.process}` string	The process the versions were collected from
`circularmapper` string	The tool name
`1.93.5` string	The command used to generate the version of the tool

Tool	Description	Homepage
circularmapper	A method to improve mappings on circular genomes such as Mitochondria.	https://circularmapper.readthedocs.io/en/latest/index.html

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:30:50 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcircularmapper%2Frealignsamfile/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/circularmapper/realignsamfile/blobs/sha256:4304c4fadf05e35c4dbd2555e96e48fa0ebd2f7fd787aba1aedcecf0963dc31a
Size	3.1 KB
Checksum	sha256:4304c4fadf05e35c4dbd2555e96e48fa0ebd2f7fd787aba1aedcecf0963dc31a
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:30:50 (UTC)		1	3.1 KB	-