mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
f080015754
* style: Add prettier config files * build: Add prettier vscode extension * ci: Replace markdownlint and yamllint with prettier * style: Run prettier * style: Use indent of 2 for markdown as well https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358 * style: Fix indent * style: Let editorconfig take over tab widths * style: yaml => yml * ci: Run prettier once Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se> Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
55 lines
1.5 KiB
YAML
55 lines
1.5 KiB
YAML
name: sistr
|
|
description: Serovar prediction of salmonella assemblies
|
|
keywords:
|
|
- bacteria
|
|
- fasta
|
|
- salmonella
|
|
tools:
|
|
- sistr:
|
|
description: Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction
|
|
homepage: https://github.com/phac-nml/sistr_cmd
|
|
documentation: https://github.com/phac-nml/sistr_cmd
|
|
tool_dev_url: https://github.com/phac-nml/sistr_cmd
|
|
doi: "10.1371/journal.pone.0147101"
|
|
licence: ["Apache-2.0"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fasta:
|
|
type: file
|
|
description: Nucleotide or protein sequences in FASTA format
|
|
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.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"
|
|
- tsv:
|
|
type: file
|
|
description: SISTR serovar prediction
|
|
pattern: "*.{tsv}"
|
|
- allele_json:
|
|
type: file
|
|
description: Allele sequences and info to JSON
|
|
pattern: "*.{json}"
|
|
- allele_fasta:
|
|
type: file
|
|
description: FASTA file destination of novel cgMLST alleles
|
|
pattern: "*.{fasta}"
|
|
- cgmlst_csv:
|
|
type: file
|
|
description: CSV file destination for cgMLST allelic profiles
|
|
pattern: "*.{csv}"
|
|
|
|
authors:
|
|
- "@rpetit3"
|