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https://github.com/MillironX/nf-core_modules.git
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de997825de
* chore: use template to create fasterq module * feat: add fasterq-dump process module * docs: provide input and output descriptions * docs: add comment on `--temp` * fix: use correct variable * tests: define test output * refactor: address review comments * refactor: remove vdb-config input * chore: add new test data to config * tests: define single-end and paired-end cases * refactor: choose specific output * tests: do not expect single FASTQ for paired-end * feat: add compression * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * tests: revert the test data name * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
42 lines
1.1 KiB
YAML
42 lines
1.1 KiB
YAML
name: sratools_fasterqdump
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description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
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keywords:
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- sequencing
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- FASTQ
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- dump
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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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- sra:
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type: directory
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description: Directory containing ETL data for the given SRA.
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pattern: "*/*.sra"
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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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- 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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authors:
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- "@Midnighter"
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