Nextflow Registry | nf-core/last/mafconvert@0.0.0-6c4ed3a

nf-core/last/mafconvert @ 0.0.0-6c4ed3a

Converts MAF alignments in another format.

LAST convert alignment MAF

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

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	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:27:32 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Flast%2Fmafconvert/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/last/mafconvert/blobs/sha256:528f9df7aba521930f266d4564a35c170264dc63584d0bf5c4439c3ffea61f19
Size	3.9 KB
Checksum	sha256:528f9df7aba521930f266d4564a35c170264dc63584d0bf5c4439c3ffea61f19
Downloads	4

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:27:32 (UTC)		4	3.9 KB