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73 lines
2.4 KiB
YAML
73 lines
2.4 KiB
YAML
name: srst2_srst2
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description: |
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Short Read Sequence Typing for Bacterial Pathogens is a program designed to take Illumina sequence data,
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a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc)
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and report the presence of STs and/or reference genes.
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keywords:
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- mlst
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- typing
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- illumina
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tools:
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- srst2:
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description: "Short Read Sequence Typing for Bacterial Pathogens"
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homepage: "http://katholt.github.io/srst2/"
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documentation: "https://github.com/katholt/srst2/blob/master/README.md"
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tool_dev_url: "https://github.com/katholt/srst2"
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doi: "10.1186/s13073-014-0090-6"
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licence: ["BSD"]
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input:
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- meta:
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type: map0.2.0-4
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description: |
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Groovy Map containing sample information
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id: should be the identification number or sample name
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single_end: should be true for single end data and false for paired in data
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db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option
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e.g. [ id:'sample', single_end:false , db:'gene']
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- fasta:
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type: file
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description: |
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gzipped fasta file. If files are NOT in
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MiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise
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default is _1, i.e. expect forward reads as sample_1.fastq.gz).
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pattern: "*.fastq.gz"
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- db:
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type: file
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description: Database in FASTA format
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pattern: "*.fasta"
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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:'sample', 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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- txt:
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type: file
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description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing
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pattern: "*_fullgenes_*_results.txt"
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- txt:
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type: file
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description: A tabulated summary report of samples x genes.
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pattern: "*_genes_*_results.txt"
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- txt:
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type: file
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description: A tabulated summary report of mlst subtyping.
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pattern: "*_mlst_*_results.txt"
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- bam:
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type: file
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description: Sorted BAM file
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pattern: "*.sorted.bam"
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- pileup:
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type: file
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description: SAMtools pileup file
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pattern: "*.pileup"
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authors:
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- "@jvhagey"
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