To run VarDistJava in single sample mode vardict_workflow_single_sample.cwl should be run. vardict_workflow_single_sample.cwl will run 3 workflows to implement the example command in the original documentations as explained here: https://github.com/AstraZeneca-NGS/VarDictJava#single-sample-mode
Tool | Version | Location |
---|---|---|
ubuntu base image (alpine) | 3.8 | - |
vardict | 1.8.2 | https://github.com/AstraZeneca-NGS/VarDictJava/releases/tag/v1.8.2 |
perl | 5.26.2-r1 | https://pkgs.alpinelinux.org/package/edge/main/aarch64/perl |
r | 3.5.1 | https://pkgs.alpinelinux.org/package/edge/community/x86/R |
- CWL specification 1.0
- Use example_inputs.yaml to see the inputs to the cwl
- Example Command using toil:
> toil-cwl-runner vardict_single_sample.cwl example_inputs.yaml
If at MSK, using the JUNO cluster you can use the following command
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/vardict_1.8.2/vardict_single_sample.cwl /path/to/inputs.yaml
#Using Toil-cwl-runner
toil-cwl-runner --singularity vardict_single_sample.cwl example_inputs.yaml
> toil-cwl-runner vardict_single_sample.cwl --help
usage: vardict_single_sample.cwl [-h] [--bedfile BEDFILE]
[--input_bam_control INPUT_BAM_CONTROL]
--input_bam_case INPUT_BAM_CASE
--reference_fasta REFERENCE_FASTA
[--sample_name SAMPLE_NAME]
[--bed_file_column_for_region_start BED_FILE_COLUMN_FOR_REGION_START]
[--bed_file_column_for_region_end BED_FILE_COLUMN_FOR_REGION_END]
[--bed_file_column_for_gene_name BED_FILE_COLUMN_FOR_GENE_NAME]
[--bed_file_column_for_chromsome BED_FILE_COLUMN_FOR_CHROMSOME]
--control_sample_name CONTROL_SAMPLE_NAME
[--filter_variants]
[--minimum_allele_frequency MINIMUM_ALLELE_FREQUENCY]
--output_vcf OUTPUT_VCF
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--bedfile BEDFILE
--input_bam_control INPUT_BAM_CONTROL
--input_bam_case INPUT_BAM_CASE
--reference_fasta REFERENCE_FASTA
--sample_name SAMPLE_NAME
--bed_file_column_for_region_start BED_FILE_COLUMN_FOR_REGION_START
--bed_file_column_for_region_end BED_FILE_COLUMN_FOR_REGION_END
--bed_file_column_for_gene_name BED_FILE_COLUMN_FOR_GENE_NAME
--bed_file_column_for_chromsome BED_FILE_COLUMN_FOR_CHROMSOME
--control_sample_name CONTROL_SAMPLE_NAME
--filter_variants
--minimum_allele_frequency MINIMUM_ALLELE_FREQUENCY
--output_vcf OUTPUT_VCF