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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
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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.
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keywords:
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- AMP
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- antimicrobial peptides
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- genome mining
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- metagenomes
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- peptide prediction
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tools:
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- macrel:
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description: A pipeline for AMP (antimicrobial peptide) prediction
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homepage: https://macrel.readthedocs.io/en/latest/
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documentation: https://macrel.readthedocs.io/en/latest/
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tool_dev_url: https://github.com/BigDataBiology/macrel
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doi: "10.7717/peerj.10555"
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licence: ['MIT']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: A fasta file with nucleotide sequences.
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pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- amp_prediction:
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type: file
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description: A zipped file, with all predicted amps in a table format.
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pattern: "*.prediction.gz"
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- smorfs:
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type: file
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description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs.
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pattern: "*.smorfs.faa.gz"
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- all_orfs:
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type: file
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description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs.
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pattern: "*.all_orfs.faa.gz"
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- readme_file:
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type: file
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description: A readme file containing tool specific information (e.g. citations, details about the output, etc.).
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pattern: "*.md"
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- log_file:
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type: file
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description: A log file containing the information pertaining to the run.
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pattern: "*_log.txt"
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authors:
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- "@darcy220606"
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