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07c0830057
* chore: apply module template * refactor: add NCBI settings to options * docs: complete meta information * feat: add prefetch process * fix: correct bash commands * tests: define the right tests * style: move option definition to satisfy linting * fix: extract version correctly * fix: correct newline issues * refactor: address review comments * Apply suggestions from code review * chore: add retrying via nf-core label * refactor: validate download thoroughly * refactor: remove vdb-config input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
43 lines
1.1 KiB
YAML
43 lines
1.1 KiB
YAML
name: sratools_prefetch
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description: Download sequencing data from the NCBI Sequence Read Archive (SRA).
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keywords:
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- sequencing
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- fastq
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- prefetch
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tools:
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- sratools:
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description: SRA Toolkit and SDK from NCBI
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homepage: https://github.com/ncbi/sra-tools
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documentation: https://github.com/ncbi/sra-tools/wiki
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tool_dev_url: https://github.com/ncbi/sra-tools
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licence: ['Public Domain']
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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: val
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description: >
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A string denoting an SRA id.
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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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- sra:
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type: directory
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description: >
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Directory containing the ETL data for the given SRA id.
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pattern: "*/*.sra"
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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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