Nextflow Registry | nf-core/last/mafconvert@0.0.0-0c7146d

nf-core/last/mafconvert @ 0.0.0-0c7146d

Converts MAF alignments in another format.

LAST convert alignment MAF

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @aleksandrabliznina @charles-plessy

Maintainers: @charles-plessy

Converts MAF alignments in another format.

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

include { LAST_MAFCONVERT } from 'nf-core/last/mafconvert'

MIT License

Process

`Name`	`LAST_MAFCONVERT`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`maf` file	Multiple Alignment Format (MAF) file, optionally compressed with gzip `*.{maf.gz,maf}`
`format` string	Output format (one of axt, bam, blast, blasttab, cram, chain, gff, html, psl, sam, or tab)

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	Genome file in FASTA format for CRAM conversion. If compressed it must be done in BGZF format (like with the bgzip tool). `*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fai` file	Genome index file needed for CRAM conversion. `*.fai`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`gzi` file	Genome index file needed for CRAM conversion when the genome file was compressed with the BGZF algorithm. `*.gzi`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`dict` file	Samtools dictionary of the genome file. `*.dict`

Output 2 channels

#1 alignment tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}` file	Pairwise alignment exported to Axt, BAM, BED, BLAST, Chain, CRAM, GFF, HTML PSL, SAM or Tab format. `*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}`

#2 versions_last tuple

`${task.process}` string	The name of the process
`last` string	The name of the tool
`lastal --version \| sed 's/lastal //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
last	LAST finds & aligns related regions of sequences.	https://gitlab.com/mcfrith/last

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:51:50 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Flast%2Fmafconvert/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/last/mafconvert/blobs/sha256:8ae1e558ce1263bbb5b946c1fcfbc57b8bcca89cf4acff862fa6a1e5f91b19c0
Size	3.9 KB
Checksum	sha256:8ae1e558ce1263bbb5b946c1fcfbc57b8bcca89cf4acff862fa6a1e5f91b19c0
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:51:50 (UTC)		1