Description

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

Input

name:type
description
pattern

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

name:type
description
pattern

sample_dir

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.

/*

contig_gbks

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/contig_gbks/:directory

The output subdirectory that contains the gbk files containing the AMP hits for each sample.

/*/contig_gbks

db_tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/${prefix}_mmseqs_matches.tsv:file

An alignment file containing the results from the MMseqs2 alignment step done on all AMP hits.

/*/*_mmseqs_matches.tsv

tsv

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/${prefix}_ampcombi.tsv:file

A file containing the summary report of all predicted AMP hits from all AMP tools given as input, the corresponding taxonomic and functional classification from the alignment step and the estimated physiochemical properties.

/*/*_ampcombi.tsv

faa

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/${prefix}_amp.faa:file

A fasta file containing the amino acid sequences of all predicted AMP hits.

/*/*_amp.faa

sample_log

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

${prefix}/${prefix}_ampcombi.log:file

A log file that captures the standard output per sample in a log file. Can be activated by --log.

/*/*.log

full_log

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

db

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

db_txt

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

amp_${opt_amp_db}_database/*.txt:file

AMP reference database in tsv-format with two columns containing header and sequence.

/amp_*_database/*.txt

db_fasta

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

amp_${opt_amp_db}_database/*.fasta:file

AMP reference database fasta file in clean format.

/amp_*_database/*.fasta

db_mmseqs

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

amp_${opt_amp_db}_database/mmseqs2/:directory

As alignment to the reference database is carried out by MMseqs2, this directory contains all the files generated by MMseqs2 on the fasta file of the database.

/amp_*_database/mmseqs2

versions

versions.yml:file

File containing software versions

versions.yml

Tools

ampcombi2/parsetables
MIT

A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format.

github.com/Darcy220606/AMPcombi ampcombi.readthedocs.io/en/main https://github.com/Darcy220606/AMPcombi/tree/dev
included in
funcscan
maintainer
Github user darcy220606
get in touch
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