Workflow Description
Simplified gatk alignment workflow.
Macros Interface
Macro Name Description
R1 r1 end of paired fastq file
R2 r2 end of paired fastq file
SAMPLE_NAME sample name
ID sample id
LIBRARY sample library
PLATFORM sequencing platform,eg.Ilumina
BWA path of bwa bin
SAMTOOLS path of samtools bin
GATK4 path of gatk4 bin(gatk)
REF path of reference genome
GATK4_BASERECALIBRATE_PARAMS gatk4 BaseRecalibrator params
PICARD path of picard jar
THREAD bwa thread
TMP tmp directory (need enough disk space to write cache file)


Zhang Yu