maf_annotated_by_tsv_0.2.3

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

Tool	Version	Location
postprocessing_variant_calls	0.2.3	ghcr.io/msk-access/postprocessing_variant_calls:0.2.3

CWL

• CWL specification 1.0

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

• Example Command using toil:

    > toil-cwl-runner maf_annotated_by_tsv.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/maf_annotated_by_tsv.cwl /path/to/inputs.yaml

#Using toil-cwl-runner
> mkdir mafAnnotation_toil_log
> toil-cwl-runner --singularity --logFile /path/to/mafAnnotation_toil_log/cwltoil.log  --jobStore /path/to/mafAnnotation_jobStore --batchSystem lsf --workDir /path/to/mafAnnotation_toil_log --outdir . --writeLogs /path/to/mafAnnotation_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/maf_annotated_by_tsv.cwl /path/to/inputs.yaml > mafAnnotation_toil.stdout 2> mafAnnotation_toil.stderr &

Usage

usage: maf_annotated_by_tsv.cwl
       [-h] [--memory_per_job MEMORY_PER_JOB]
       [--memory_overhead MEMORY_OVERHEAD]
       [--number_of_threads NUMBER_OF_THREADS] --input_maf INPUT_MAF
       [--output_maf_name OUTPUT_MAF_NAME]
       [--output_column_name OUTPUT_COLUMN_NAME] --input_tsv_file
       INPUT_TSV_FILE [--separator SEPARATOR]
       [job_order]

pv_maf_annotated_by_tsv

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
  --input_maf INPUT_MAF
  --output_maf_name OUTPUT_MAF_NAME
  --output_column_name OUTPUT_COLUMN_NAME
  --input_tsv_file INPUT_TSV_FILE
  --separator SEPARATOR