Nextflow Registry | nf-core/macsyfinder/search@0.0.0-6c4ed3a

nf-core/macsyfinder/search @ 0.0.0-6c4ed3a

Search for macromolecular systems in protein datasets using MacSyFinder

genomics protein macromolecular systems hmmer search

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @brovolia

Maintainers: @brovolia

Search for macromolecular systems in protein datasets using MacSyFinder

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

include { MACSYFINDER_SEARCH } from 'nf-core/macsyfinder/search'

MIT License

Process

`Name`	`MACSYFINDER_SEARCH`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test' ]`
`proteins` file	Protein sequence file in FASTA format `*.{fasta,faa,fa}`

`models` directory	Directory containing MacSyFinder model(s) `*`

`model_names` string	Space-separated list of model names to search for. If not provided, all models in the directory will be used.

Output 8 channels

#1 hmmer tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', db_type:'gembase' ]`
`${prefix}/hmmer_results` directory	Directory containing HMMER search results (may contain variable content like timestamps) `${prefix}/hmmer_results`

#2 stderr tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', db_type:'gembase' ]`
`${prefix}/macsyfinder.err` file	MacSyFinder standard error `${prefix}/macsyfinder.err`

#3 stdout tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', db_type:'gembase' ]`
`${prefix}/macsyfinder.out` file	MacSyFinder standard output `${prefix}/macsyfinder.out`

#4 results tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', db_type:'gembase' ]`
`${prefix}/*` directory	Directory containing all MacSyFinder results `${prefix}/*`

#5 summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', db_type:'gembase' ]`
`${prefix}/all_systems.tsv` file	Summary table of all detected systems `${prefix}/all_systems.tsv`

#6 best_solutions tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', db_type:'gembase' ]`
`${prefix}/all_best_solutions*` file	Best solution files for detected systems `${prefix}/all_best_solutions*`

#7 versions_hmmer tuple

`${task.process}` string	The name of the process
`hmmer` string	The name of the tool
`hmmsearch -h 2>&1 \| sed "2!d;s/^# HMMER //;s/ .*$//"` eval	The expression to obtain the version of the tool

#8 versions_macsyfinder tuple

`${task.process}` string	The name of the process
`macsyfinder` string	The name of the tool
`macsyfinder --version 2>&1 \| sed "1!d;s/^.MacSyFinder //;s/ .$//"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
macsyfinder	Detection of macromolecular systems in protein datasets using systems modelling and similarity search	https://github.com/gem-pasteur/macsyfinder

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b