Tool | Version | Location |
---|---|---|
bcftools | 1.15.1 | https://github.com/samtools/bcftools/releases/tag/1.15.1 |
- CWL specification 1.0
- Use example_inputs.yaml to see the inputs to the cwl
- Example Command using toil:
toil-cwl-runner bcftools_sort_1.15.1.cwl example_inputs.yaml
If at MSK, using the JUNO cluster having installed toil version 3.19 and manually modifying lsf.py by removing type==X86_64 &&
you can use the following command
#Using CWLTOOL
cwltool --singularity --non-strict /path/to/bcftools_sort_1.15.1.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
mkdir bcftools_toil_log
toil-cwl-runner --singularity --logFile /path/to/bcftools_toil_log/cwltoil.log --jobStore /path/to/bcftools_jobStore --batchSystem lsf --workDir /path/to/bcftools_toil_log --outdir . --writeLogs /path/to/bcftools_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/bcftools_sort_1.15.1.cwl /path/to/inputs.yaml > bcftools_toil.stdout 2> bcftools_toil.stderr &
usage: toil-cwl-runner bcftools_sort_1.15.1.cwl [-h]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--memory_per_job MEMORY_PER_JOB
Memory per job in megabytes
--memory_overhead MEMORY_OVERHEAD
Memory overhead per job in megabytes
--number_of_threads NUMBER_OF_THREADS
--output_name OUTPUT_NAME
Output file name
--output_type OUTPUT_TYPE
compressed BCF (b), uncompressed BCF (u), compressed
VCF (z), uncompressed VCF (v)
--input INPUT input vcf files