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

nf-core/clipkit @ 0.0.0-0c7146d

A multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.

alignment trimming phylogeny

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @vagkaratzas

Maintainers: @vagkaratzas

A multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.

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

include { CLIPKIT } from 'nf-core/clipkit'

MIT License

Process

`Name`	`CLIPKIT`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1']`
`aln` file	Multiple sequence alignment file in various supported formats. `*.{fa,fasta,fna,faa,alnfaa,aln,sto,stk,mauve,alignment,clustal}`

`out_format` string	Output format (aln,msa,fas,etc.), default is clipkit. `*`

`auxiliary_file` file	Optional tab-delimited auxiliary file specifying which sites to keep or trim. Used in conjunction with the custom site trimming (cst) mode. `*.tsv`

Output 6 channels

#1 log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.${out_extension}.log` file	Log file with per-site trimming statistics from ClipKIT execution. `*.log`

#2 json tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.${out_extension}.report.json` file	JSON report file with summary statistics of the trimming run. Optional; only produced when ClipKIT is run with the appropriate reporting flag. `*.report.json`

#3 clipkit tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.${out_extension}` file	Trimmed multiple sequence alignment file. `.`

#4 metadata tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.${out_extension}.txt` file	Tab-delimited text file with per-site statistics including site position, parsimony-informativeness status, and whether the site was kept or trimmed. `*.txt`

#5 complementary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`${prefix}.${out_extension}.complement` file	File containing the trimmed/removed sites from the alignment, i.e. the complement of the clipkit output. Optional; only produced when the complementary input is true (passes `-c` to clipkit). `*.complement`

#6 versions_clipkit tuple

`${task.process}` string	The name of the process
`clipkit` string	The name of the tool
`clipkit --version 2>&1 \| sed 's/clipkit //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
clipkit	ClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes those with poor phylogenetic signal.	https://jlsteenwyk.com/ClipKIT/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:30:55 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fclipkit/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/clipkit/blobs/sha256:b5e720aed7e6bc741f5eb89e9b8e4ecbe49fcfca88fa4ab908b1cef102445892
Size	3.7 KB
Checksum	sha256:b5e720aed7e6bc741f5eb89e9b8e4ecbe49fcfca88fa4ab908b1cef102445892
Downloads	1