name: sratools_fasterqdump description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA). keywords: - sequencing - FASTQ - dump tools: - sratools: description: SRA Toolkit and SDK from NCBI homepage: https://github.com/ncbi/sra-tools documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ['US-Government-Work'] input: - meta: type: map description: > Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - sra: type: directory description: Directory containing ETL data for the given SRA. pattern: "*/*.sra" 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" - reads: type: file description: Extracted FASTQ file or files if the sequencing reads are paired-end. pattern: "*.fastq.gz" authors: - "@Midnighter"