0.1.1

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

Tool	Version	Location
access_utils	0.1.1	https://github.com/msk-access/access_utils/

CWL

• CWL specification 1.0

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

• Example Command using toil:

    > toil-cwl-runner general_stats_parse.cwl example_inputs.json

#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/general_stats_parse.cwl /path/to/example_inputs.json

#Using toil-cwl-runner
> mkdir tool_toil_log
> toil-cwl-runner --singularity --logFile /path/to/tool_toil_log/cwltoil.log  --jobStore /path/to/tool_jobStore --batchSystem lsf --workDir /path/to/tool_toil_log --outdir . --writeLogs /path/to/tool_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/multiqc_1.10.1/multiqc_1.10.1.cwl /path/to/example_inputs.json > tool_toil.stdout 2> tool_toil.stderr &

Usage

> toil-cwl-runner general_stats_parse.cwl -h