Nextflow Registry | nf-core/ampcombi2/parsetables@0.0.0-be790aa

nf-core/ampcombi2/parsetables @ 0.0.0-be790aa

A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.

Latest version: 0.0.0-be790aa

Total downloads: 13

Source: nf-core/modules

Authors: @darcy220606

Maintainers: @darcy220606 @jasmezz

A submodule that parses and standardizes the results from various antimicrobial peptide identification tools.

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

include { AMPCOMBI2_PARSETABLES } from 'nf-core/ampcombi2/parsetables'

MIT License

Process

`Name`	`AMPCOMBI2_PARSETABLES`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`amp_input` list	The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools. `[amptool.tsv, amptool.tsv]`

`faa_input` file	The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa `*.faa`

`gbk_input` file	The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where "sample_1" is the sample name. `*.gbk`

`opt_amp_db` string	The name of the database to download and set up. This can either be 'DRAMP', 'APD' or 'UniRef100'. `DRAMP\|APD\|UniRef100`

`opt_amp_db_dir` directory	The path to the folder containing the fasta and tsv database files. `path/to/amp_*_database`

`opt_interproscan` directory	A path to a file corresponding to the respective tsv files containing protein classifications of the annotated CDSs. The file must be the raw output from InterProScan. `*.tsv`

Output 4 channels

#1 db tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`amp_${opt_amp_db}_database/` directory	If the AMP reference database ID is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. `/amp_*_database`

#2 full_log tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`Ampcombi_parse_tables.log` file	A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. `Ampcombi_parse_tables.log`

#3 sample_dir tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}/` directory	The output directory that contains the summary output and related alignment files for one sample. `/*`

#4 versions_ampcombi tuple

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

Tool	Description	Homepage
ampcombi2/parsetables	A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.	https://github.com/paleobiotechnology/AMPcombi

Version	0.0.0-be790aa
Commit ID	be790aafaa178554b403f862164eb27042f0b35a
Release Date	24 Apr 2026 15:00:34 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fampcombi2%2Fparsetables/0.0.0-be790aa/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/ampcombi2/parsetables/blobs/sha256:b5513cd2ce0fd5c3a9f9f7cf42f39ed6dc25b026749d701dfa6edb2857f1261e