mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
1f3f2b18bb
* Add new module macrel/contigs * removed trailing whitespace * removed whitespace * linting cleanup * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Updated the test.yml It didnt upload the updated version earlier for some reason :( * Update test.yml * Update test.yml * Update test.yml as generated by pytest * Update test.yml * updated the version issue * Update tests/modules/macrel/contigs/test.yml * Update modules/macrel/contigs/main.nf * Update modules/macrel/contigs/main.nf * Update pytest_modules.yml * Update pytest_modules.yml * Update modules/macrel/contigs/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Zipped all fasta outputs * Update main.nf * Update test.yml * Update test.yml * Update main.nf * Update main.nf (gzip -n) * Update test.yml * Update main.nf * Update main.nf * Update test.yml * Update tests/modules/macrel/contigs/test.yml * Update modules/macrel/contigs/main.nf * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: darcy220606 <ananhamido@hotmail.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
61 lines
2 KiB
YAML
61 lines
2 KiB
YAML
name: macrel_contigs
|
|
description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found.
|
|
keywords:
|
|
- AMP
|
|
- antimicrobial peptides
|
|
- genome mining
|
|
- metagenomes
|
|
- peptide prediction
|
|
tools:
|
|
- macrel:
|
|
description: A pipeline for AMP (antimicrobial peptide) prediction
|
|
homepage: https://macrel.readthedocs.io/en/latest/
|
|
documentation: https://macrel.readthedocs.io/en/latest/
|
|
tool_dev_url: https://github.com/BigDataBiology/macrel
|
|
doi: "10.7717/peerj.10555"
|
|
licence: ['MIT']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fasta:
|
|
type: file
|
|
description: A fasta file with nucleotide sequences.
|
|
pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- amp_prediction:
|
|
type: file
|
|
description: A zipped file, with all predicted amps in a table format.
|
|
pattern: "*.prediction.gz"
|
|
- smorfs:
|
|
type: file
|
|
description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.
|
|
pattern: "*.smorfs.faa.gz"
|
|
- all_orfs:
|
|
type: file
|
|
description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.
|
|
pattern: "*.all_orfs.faa.gz"
|
|
- readme_file:
|
|
type: file
|
|
description: A readme file containing tool specific information (e.g. citations, details about the output, etc.).
|
|
pattern: "*.md"
|
|
- log_file:
|
|
type: file
|
|
description: A log file containing the information pertaining to the run.
|
|
pattern: "*_log.txt"
|
|
|
|
authors:
|
|
- "@darcy220606"
|