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: 0.0.0-6c4ed3a

Total downloads: 9

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	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 18:51:54 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fcircularmapper%2Frealignsamfile/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/circularmapper/realignsamfile/blobs/sha256:c40e339ebd92fc0d722594a166351b495a8d0f7978b1263652e560a0991769e7
Size	3.1 KB
Checksum	sha256:c40e339ebd92fc0d722594a166351b495a8d0f7978b1263652e560a0991769e7
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:09:16 (UTC)	3	3.1 KB
0.0.0-3fc6d40	22 Apr 2026 15:05:57 (UTC)	3	3.2 KB
0.0.0-0c7146d	08 Apr 2026 18:51:54 (UTC)	3	3.1 KB