Nextflow Registry | nf-core/ampcombi@0.0.0-6c4ed3a

nf-core/ampcombi @ 0.0.0-6c4ed3a

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

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @darcy220606 @louperelo

Maintainers: @darcy220606 @louperelo

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

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

include { AMPCOMBI } from 'nf-core/ampcombi'

MIT License

Process

`Name`	`AMPCOMBI`

Input 3 channels

#1 tuple

`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 12 channels

#1 csv tuple

`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`

#2 faa tuple

`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`

#3 log tuple

`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`

#4 txt tuple

`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`

#5 results_db tuple

`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`

#6 sample_dir tuple

`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. `/*`

#7 summary_csv tuple

`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`

#8 summary_html tuple

`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`

#9 results_db_tsv tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`amp_ref_database/*.tsv` file	AMP reference da