Download sequencing data from the NCBI Sequence Read Archive (SRA).
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
id{:bash}
:string
A string denoting an SRA id.
ncbi_settings{:bash}
:file
An NCBI user settings file.
*.mkfg
certificate{:bash}
Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit
*.cart
sra{:bash}
${id}{:bash}
:directory
Directory containing SRA data files
*/*.sra
versions_sratools{:bash}
${task.process}{:bash}
The name of the process
sratools{:bash}
The name of the tool
prefetch --version 2>&1 | grep -Eo '[0-9.]+'{:bash}
:eval
The expression to obtain the version of the tool
versions_curl{:bash}
curl{:bash}
curl --version | sed '1!d;s/^curl //; s/ .*//'{:bash}
versions{:bash}
SRA Toolkit and SDK from NCBI
