Nextflow Registry | nf-core/cmaple@0.0.0-0c7146d

nf-core/cmaple @ 0.0.0-0c7146d

Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @vagkaratzas

Maintainers: @vagkaratzas

Efficient phylogenetic tree reconstruction for sequences using the CMAPLE algorithm

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

include { CMAPLE } from 'nf-core/cmaple'

MIT License

Process

`Name`	`CMAPLE`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`aln` file	Multiple sequence alignment file in FASTA, PHYLIP, or MAPLE format. Can be gzipped on uncompressed. `*.{fa,fasta,faa,fna,fas,aln,afa,phy,phylip,maple}{.gz,}`
`newick` file	A Newick formatted tree based on multiple sequence alignment `*.{newick,nwk,treefile}`

Output 3 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.log` file	Log file containing detailed information about the tree reconstruction process `*.log`

#2 treefile tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.treefile` file	Maximum likelihood phylogenetic tree in Newick format `*.treefile`

#3 versions_cmaple tuple

`${task.process}` string	The name of the process
`cmaple` string	The name of the tool
`cmaple --help \| grep -m1 -oE "[0-9]+(\.[0-9]+)+"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
cmaple	CMAPLE (Comprehensive Maximum-likelihood Analysis for Phylogenetic Likelihood Estimation) is an efficient implementation of the MAPLE algorithm for phylogenetic tree reconstruction, particularly optimized for pathogen sequences with low divergence such as SARS-CoV-2. It is integrated within IQ-TREE.	https://github.com/iqtree/cmaple

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:31:06 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fcmaple/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/cmaple/blobs/sha256:8b685b30e9e361d91461327e9281d29415e62725c49314053c2157bf97a5dc40
Size	2.9 KB
Checksum	sha256:8b685b30e9e361d91461327e9281d29415e62725c49314053c2157bf97a5dc40
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:31:06 (UTC)		1	2.9 KB	-