bcftools norm v1.15.1

Version of tools in docker image (/container/Dockerfile)

Tool	Version	Location
bcftools	1.15.1	https://github.com/samtools/bcftools/releases/tag/1.15.1

CWL

• CWL specification 1.0

• Use example_inputs.yaml to see the inputs to the cwl

• Example Command using toil:

toil-cwl-runner bcftools_norm_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_norm_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_norm_1.15.1.cwl /path/to/inputs.yaml > bcftools_toil.stdout 2> bcftools_toil.stderr &

Usage

usage: toil-cwl-runner bcftools_norm_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
  --check_ref CHECK_REF
  --multiallelics MULTIALLELICS
                        use any
  --output_type OUTPUT_TYPE
  --output_name OUTPUT_NAME
  --input INPUT         input vcf file
  --fastaRef FASTAREF