Tool | Version | Location |
---|---|---|
java base image | 8 | - |
waltz | 3.1.1 | https://github.com/juberpatel/Waltz/releases/download/v3.1.1/Waltz-3.1.1.jar |
- CWL specification 1.0
- Use example_inputs.yml to see the inputs to the cwl
- Example Command using toil:
> toil-cwl-runner waltz_count_reads_3.1.1.cwl example_inputs.yml
If at MSK, using the JUNO cluster you can use the following command
#Using CWLTOOL
> cwltool --singularity --non-strict waltz_count_reads_3.1.1.cwl inputs.yaml
#Using toil-cwl-runner
> mkdir run_directory
> toil-cwl-runner --singularity --logFile path/to/run_directory/cwltoil.log --jobStore path/to/jobStore --batchSystem lsf --workDir /path/to/run_directory --outdir /path/to/run_directory --writeLogs /path/to/run_directory --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 waltz_count_reads_3.1.1.cwl inputs.yaml > file.stdout 2> file.stderr &
> toil-cwl-runner waltz_count_reads_3.1.1.cwl --help
usage: waltz_count_reads_3.1.1.cwl [-h] --bam BAM --gene_list GENE_LIST
[--coverage_threshold COVERAGE_THRESHOLD]
[--memory_per_job MEMORY_PER_JOB]
[--memory_overhead MEMORY_OVERHEAD]
[--number_of_threads NUMBER_OF_THREADS]
--bed_file BED_FILE
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--bam BAM
--gene_list GENE_LIST
--coverage_threshold COVERAGE_THRESHOLD
--memory_per_job MEMORY_PER_JOB
--memory_overhead MEMORY_OVERHEAD
--number_of_threads NUMBER_OF_THREADS
--bed_file BED_FILE