Nextflow Registry | nf-core/tcoffee/tcs@0.0.0-0c7146d

nf-core/tcoffee/tcs @ 0.0.0-0c7146d

Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.

alignment MSA evaluation

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @alessiovignoli

Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.

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

include { TCOFFEE_TCS } from 'nf-core/tcoffee/tcs'

MIT License

Process

`Name`	`TCOFFEE_TCS`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', ... ]
`msa` file	fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. `*.{aln,fa,fasta,fas}{.gz,}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`lib` file	lib file containing the alignment library of the given msa. `{.tc_lib,_lib}`

Output 4 channels

#1 tcs tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.tcs` file	The msa represented in tcs format, prepended with TCS scores `*.tcs`

#2 scores tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.scores` file	a file containing the score of the alignment in csv format `*.scores`

#3 versions_pigz tuple

`${task.process}` string	The name of the process
`pigz` string	The name of the tool
`pigz --version 2>&1 \| sed "s/^.pigz[[:space:]]//"` eval	The expression to obtain the version of the tool

#4 versions_tcoffee tuple

`${task.process}` string	The name of the process
`tcoffee` string	The name of the tool
`t_coffee -version \| awk '{gsub("Version_", ""); print \$3}'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
tcoffee	A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence	http://www.tcoffee.org/Projects/tcoffee/
pigz	Parallel implementation of the gzip algorithm.	https://zlib.net/pigz/

Version	0.0.0-0c7146d
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	08 Apr 2026 19:43:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Ftcoffee%2Ftcs/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/tcoffee/tcs/blobs/sha256:0ac18a628a3639c82c610e8254f2313cc431acadcc3c8340473005ec2e2c4565
Size	3.5 KB
Checksum	sha256:0ac18a628a3639c82c610e8254f2313cc431acadcc3c8340473005ec2e2c4565
Downloads	3

Version	Date	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:49:36 (UTC)	3	3.6 KB
0.0.0-3fc6d40	22 Apr 2026 15:34:24 (UTC)	3	3.6 KB
0.0.0-0c7146d	08 Apr 2026 19:43:22 (UTC)	3	3.5 KB