Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
sra
:directory
Directory containing ETL data for the given SRA.
*/*.sra
ncbi_settings
:file
An NCBI user settings file.
*.mkfg
certificate
Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
*.cart
reads
*.fastq.gz
Extracted FASTQ file or files if the sequencing reads are paired-end.
versions_sratools
${task.process}
:string
The name of the process
sratools
The name of the tool
prefetch --version 2>&1 | grep -Eo '[0-9.]+'
:eval
The expression to obtain the version of the tool
versions_pigz
pigz
pigz --version 2>&1 | sed 's/pigz //g'
versions
SRA Toolkit and SDK from NCBI
