Nextflow Registry | nf-core/segemehl/align@0.0.0-0c7146d

nf-core/segemehl/align @ 0.0.0-0c7146d

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

alignment circrna splicing fusions

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @BarryDigby @nictru

Maintainers: @nictru

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

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

include { SEGEMEHL_ALIGN } from 'nf-core/segemehl/align'

MIT License

Process

`Name`	`SEGEMEHL_ALIGN`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reads` file	FASTA or FASTQ files `*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}`

`fasta` file	Reference genome FASTA file used to construct Segemehl `*.{fa,fasta}`

`index` file	Segemehl Index file from SEGEMEHL_INDEX `*.idx`

Output 5 channels

#1 versions

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

#2 alignment tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.${suffix}` file	File containing genomic alignments in SAM format (please add "-b" flag to task.ext.args for BAM) `*.{sam,bam}`

#3 multi_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.mult.bed` file	Bed file containing all splice events predicted in the split read alignments. (optional, only if -S flag is set in task.ext.args) `*.mult.bed`

#4 single_bed tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.sngl.bed` file	Bed file containing all single splice events predicted in the split read alignments. (optional, only if -S flag is set in task.ext.args) `*.sngl.bed`

#5 trans_alignments tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}/${prefix}.trns.txt` file	Custom text file containing all single split alignments predicted to be in trans (optional, only if -S flag is set in task.ext.args) `*.trns.txt`

Tool	Description	Homepage
segemehl	A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection	https://www.bioinf.uni-leipzig.de/Software/segemehl/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:35:29 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fsegemehl%2Falign/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/segemehl/align/blobs/sha256:e630a6a446f1252ab81e3243e895989c0f24fd3fa95ad3595173431cf85829c1
Size	2.9 KB
Checksum	sha256:e630a6a446f1252ab81e3243e895989c0f24fd3fa95ad3595173431cf85829c1
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:43:46 (UTC)	4	2.9 KB
0.0.0-3fc6d40	22 Apr 2026 15:30:08 (UTC)	3	2.9 KB
0.0.0-0c7146d	08 Apr 2026 19:35:29 (UTC)	3	2.9 KB