Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads
:file
Input Illunina paired-end FASTQ files
*.{fq.gz,fastq.gz}
xml
Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
[ id:'test', single_end:false ]
*.xml
The predicted serotype in XML format
txt
*.txt
A detailed description of the predicted serotype
versions_pneumocat
${task.process}
:string
The name of the process
pneumocat
The name of the tool
1.2.1
The expression to obtain the version of the tool
versions
PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)
