MultiQC v1.10.1.7

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

Tool	Version	Location
multiqc	1.10.1.7	https://github.com/msk-access/MultiQC/

CWL

• CWL specification 1.0

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

• Example Command using toil:

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

#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/multiqc_1.10.1.7/multiqc.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 multiqc.cwl --helpusage: multiqc_1.10.1.cwl [-h]
                          [--qc_files_array_of_array QC_FILES_ARRAY_OF_ARRAY]
                          [--qc_files_dir QC_FILES_DIR]
                          [--qc_list_of_dirs QC_LIST_OF_DIRS]
                          [--report_name REPORT_NAME] [--config CONFIG]
                          [job_order]

Run multiqc on log files from supported bioinformatic tools.

positional arguments:
  job_order             Job input json file

optional arguments:
  -h, --help            show this help message and exit
  --qc_files_array_of_array QC_FILES_ARRAY_OF_ARRAY
                        qc files which shall be part of the multiqc summary;
                        optional, only one of qc_files_array or
                        qc_files_array_of_array must be provided
  --qc_files_dir QC_FILES_DIR
                        qc files in a Directory
  --qc_list_of_dirs QC_LIST_OF_DIRS
                        qc files in multiple directories
  --report_name REPORT_NAME
                        name used for the html report
  --config CONFIG