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mskcc / cwl-commandlinetools

Central location for CWL CommandLineTools
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Feature/add octopus #93

Closed karthigayini closed 2 years ago

karthigayini commented 2 years ago

CWL And Docker For Running Octopus

Version of tools in docker image

Tool Version Location
Octopus v0.7.4 ghcr.io/msk-access/octopus:0.7.4

CWL

CWL specification 1.0 Use example_input.yaml to see the inputs to the cwl Example Command using toil: toil-cwl-runner octopus_0-7-4.cwl example_input.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/mutect_1.1.5.cwl /path/to/inputs.yaml

Using toil-cwl-runner

mkdir octopus_toil_log
toil-cwl-runner --singularity --logFile /path/to/octopus_toil_log/cwltoil.log  --jobStore /path/to/octopus_jobStore --batchSystem lsf --workDir /path/to/octopus_toil_log --outdir . --writeLogs /path/to/octopus_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/octopus_0-7-4.cwl /path/to/inputs.yaml > octopus_toil.stdout 2> octopus_toil.stderr &

Usage

usage: /work/bergerm1/bergerlab/sivaprk/tool_testing/octopus_full.cwl
       [-h] --input INPUT [--normalId NORMALID] [--tumorOnlySample]
       [--somaticOnlyCalls]
       [--targettedCalling_singleEntry TARGETTEDCALLING_SINGLEENTRY]
       [--skipRegions_singleEntry SKIPREGIONS_SINGLEENTRY]
       [--targettedCalling_file TARGETTEDCALLING_FILE]
       [--skipRegions_file SKIPREGIONS_FILE] [--error_models ERROR_MODELS]
       --reference REFERENCE --output_file_name OUTPUT_FILE_NAME