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41 lines
999 B
YAML
41 lines
999 B
YAML
name: sra_fastq
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description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
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keywords:
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- SRA
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- NCBI
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- sequencing
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- FASTQ
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- prefetch
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- fasterq-dump
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modules:
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- custom/sratoolsncbisettings
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- sratools/prefetch
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- sratools/fasterqdump
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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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- id:
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type: string
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description: >
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SRA run identifier.
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# TODO Update when we decide on a standard for subworkflow docs
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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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- reads:
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type: file
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description: Extracted FASTQ file or files if the sequencing reads are paired-end.
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pattern: "*.fastq.gz"
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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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authors:
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- "@Midnighter"
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