modules/ampcombi2_parsetables

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

antimicrobial peptidesampsparsingreportingalignmacrelamplifyhmmsearchneubiampirampgramamptransformerDRAMPMMseqs2InterProScan

https://github.com/nf-core/modules/[...]/modules/nf-core/ampcombi2/parsetables

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.

/*

`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

`versions_ampcombi`

`${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

Topics

name:type

description

pattern

`versions`

`${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

Tools

ampcombi2/parsetables
MIT

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

github.com/paleobiotechnology/AMPcombi ampcombi.readthedocs.io https://github.com/paleobiotechnology/AMPcombi/tree/dev

modules/ampcombi2_parsetables

Description

Input

`meta`
`:map`

`amp_input`
`:list`

`faa_input`
`:file`

`gbk_input`
`:file`

`opt_amp_db`
`:string`

`opt_amp_db_dir`
`:directory`

`opt_interproscan`
`:directory`

Output

`sample_dir`

`meta`
`:map`

`${prefix}/`
`:directory`

`full_log`

`meta`
`:map`

`Ampcombi_parse_tables.log`
`:file`

`db`

`meta`
`:map`

`amp_${opt_amp_db}_database/`
`:directory`

`versions_ampcombi`

`${task.process}`
`:string`

`ampcombi`
`:string`

`ampcombi --version | sed 's/ampcombi //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`ampcombi`
`:string`

`ampcombi --version | sed 's/ampcombi //'`
`:eval`

Tools

ampcombi2/parsetables
MIT

included in

maintainers

get in touch

modules/ampcombi2_parsetables

Description

Input

meta:map

amp_input:list

faa_input:file

gbk_input:file

opt_amp_db:string

opt_amp_db_dir:directory

opt_interproscan:directory

Output

sample_dir

meta:map

${prefix}/:directory

full_log

meta:map

Ampcombi_parse_tables.log:file

db

meta:map

amp_${opt_amp_db}_database/:directory

versions_ampcombi

${task.process}:string

ampcombi:string

ampcombi --version | sed 's/ampcombi //':eval

Topics

versions

${task.process}:string

ampcombi:string

ampcombi --version | sed 's/ampcombi //':eval

Tools

ampcombi2/parsetables MIT

included in

maintainers

get in touch

`meta`
`:map`

`amp_input`
`:list`

`faa_input`
`:file`

`gbk_input`
`:file`

`opt_amp_db`
`:string`

`opt_amp_db_dir`
`:directory`

`opt_interproscan`
`:directory`

`sample_dir`

`meta`
`:map`

`${prefix}/`
`:directory`

`full_log`

`meta`
`:map`

`Ampcombi_parse_tables.log`
`:file`

`db`

`meta`
`:map`

`amp_${opt_amp_db}_database/`
`:directory`

`versions_ampcombi`

`${task.process}`
`:string`

`ampcombi`
`:string`

`ampcombi --version | sed 's/ampcombi //'`
`:eval`

`versions`

`${task.process}`
`:string`

`ampcombi`
`:string`

`ampcombi --version | sed 's/ampcombi //'`
`:eval`

ampcombi2/parsetables
MIT