Get reference to run Personal Cancer Genome Reporter (PCGR)
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
bundleversion
:string
PCGR reference data bundle version
*[0-9]*
genome
:string
PCGR reference genome version
grch37|grch38
Output
name:type
description
pattern
pcgrref
meta
:map
Groovy Map containing sample information
e.g. [ id:'sample1' ]
${bundleversion}
:directory
PCGR reference data directory
{bundleversion}/
versions_curl
${task.process}
:string
The process the versions were collected from
curl
:string
The tool name
curl --version | head -1 | cut -d ' ' -f 2
:string
The command used to generate the version of the tool
versions_gzip
${task.process}
:string
The process the versions were collected from
gzip
:string
The tool name
gzip --version | head -1 | cut -d ' ' -f 2
:string
The command used to generate the version of the tool
versions_tar
${task.process}
:string
The process the versions were collected from
tar
:string
The tool name
tar --version | head -1 | cut -d ' ' -f 4
:string
The command used to generate the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The process the versions were collected from
curl
:string
The tool name
curl --version | head -1 | cut -d ' ' -f 2
:string
The command used to generate the version of the tool
${task.process}
:string
The process the versions were collected from
gzip
:string
The tool name
gzip --version | head -1 | cut -d ' ' -f 2
:string
The command used to generate the version of the tool
${task.process}
:string
The process the versions were collected from
tar
:string
The tool name
tar --version | head -1 | cut -d ' ' -f 4
:string
The command used to generate the version of the tool
Tools
pcgr
MIT
The Personal Cancer Genome Reporter (PCGR) is a stand-alone software package for functional annotation and translation of individual tumor genomes for precision cancer medicine
