modules/ampcombi

A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.

antimicrobial peptidesampsparsingreportingalignmacrelamplifyhmmsearchneubiampirDRAMP

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

Description

A tool to parse and summarise results from antimicrobial peptides tools and present functional classification.

Input

name:type

description

pattern

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`amp_input:list`

The path to the directory containing the results for the AMP tools for each sample processed 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

`opt_amp_db:directory`

The path to the folder containing the fasta and tsv database files.

*/

Output

name:type

description

pattern

`sample_dir`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${meta.id}/:directory`

The output directory that contains the summary output and related alignment files for one sample.

/*

`txt`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${meta.id}/*diamond_matches.txt:file`

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

/*/*_diamond_matches.txt

`csv`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${meta.id}/*ampcombi.csv:file`

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

/*/*_ampcombi.csv

`faa`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`${meta.id}/*amp.faa:file`

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

/*/*_amp.faa

`summary_csv`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`AMPcombi_summary.csv:file`

A file that concatenates all samples ampcombi summaries. This is activated with --complete_summary true.

AMPcombi_summary.csv

`summary_html`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`AMPcombi_summary.html:file`

A file that concatenates all samples ampcombi summaries. This is activated with --complete_summary true.

AMPcombi_summary.html

`log`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`*.log:file`

A log file that captures the standard output ina log file. Can be activated by --log.

*.log

`results_db`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`amp_ref_database/:directory`

If the AMP reference database 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_ref_database

`results_db_dmnd`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`amp_ref_database/*.dmnd:file`

AMP reference database converted to DIAMOND database format.

/amp_ref_database/*.dmnd

`results_db_fasta`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`amp_ref_database/*.clean.fasta:file`

AMP reference database fasta file, cleaned of diamond-incompatible characters.

/amp_ref_database/*.clean.fasta

`results_db_tsv`

`meta:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`amp_ref_database/*.tsv:file`

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

/amp_ref_database/*.tsv

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

ampcombi
MIT

This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications.

github.com/Darcy220606/AMPcombi https://github.com/Darcy220606/AMPcombi/tree/dev

modules/ampcombi

Description

Input

meta:map

amp_input:list

faa_input:file

opt_amp_db:directory

Output

sample_dir

meta:map

${meta.id}/:directory

txt

meta:map

${meta.id}/*diamond_matches.txt:file

csv

meta:map

${meta.id}/*ampcombi.csv:file

faa

meta:map

${meta.id}/*amp.faa:file

summary_csv

meta:map

AMPcombi_summary.csv:file

summary_html

meta:map

AMPcombi_summary.html:file

log

meta:map

*.log:file

results_db

meta:map

amp_ref_database/:directory

results_db_dmnd

meta:map

amp_ref_database/*.dmnd:file

results_db_fasta

meta:map

amp_ref_database/*.clean.fasta:file

results_db_tsv

meta:map

amp_ref_database/*.tsv:file

versions

versions.yml:file

Tools

ampcombi MIT

maintainers

get in touch

`meta:map`

`amp_input:list`

`faa_input:file`

`opt_amp_db:directory`

`sample_dir`

`meta:map`

`${meta.id}/:directory`

`txt`

`meta:map`

`${meta.id}/*diamond_matches.txt:file`

`csv`

`meta:map`

`${meta.id}/*ampcombi.csv:file`

`faa`

`meta:map`

`${meta.id}/*amp.faa:file`

`summary_csv`

`meta:map`

`AMPcombi_summary.csv:file`

`summary_html`

`meta:map`

`AMPcombi_summary.html:file`

`log`

`meta:map`

`*.log:file`

`results_db`

`meta:map`

`amp_ref_database/:directory`

`results_db_dmnd`

`meta:map`

`amp_ref_database/*.dmnd:file`

`results_db_fasta`

`meta:map`

`amp_ref_database/*.clean.fasta:file`

`results_db_tsv`

`meta:map`

`amp_ref_database/*.tsv:file`

`versions`

`versions.yml:file`

ampcombi
MIT