WDL wrapper for running the PanGenie tool. Read more at PanGenie for tool usage and general information, and at Docker Hub for running the tool using docker.
- FORWARD_FASTQ: compressed R1 FASTQ file
- REVERSE_FASTQ: compressed R2 FASTQ file
- SAMPLE_NAME: the sample name
- PANGENOME_VCF: the input vcf with variants to be genotyped
- REF_GENOME: a FASTA file of the reference genome for variant calling
- SORT_INDEX_OUTPUT_VCF: Should the output VCF be sorted, bgzipped and indexed? Default is true. If false, the output VCF is just gzipped.
For example with cromwell or miniwdl, and using the small test dataset in the test folder:
miniwdl run --as-me --copy-input-files PanGenie.wdl -i inputs.json
## or
java -jar $CROMWELL_JAR run PanGenie.wdl -i inputs.json