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2.27](https://bedtools.readthedocs.io/en/latest/)\n* [freec 11.5](https://github.com/BoevaLab/FREEC/archive/v11.5.tar.gz)\n\n\n## Usage\n\n### Cromwell\n```\njava -jar cromwell.jar run freec.wdl --inputs inputs.json\n```\n\n### Inputs\n\n#### Required workflow parameters:\nParameter|Value|Description\n---|---|---\n`inputTumor`|File|Input .bam file for analysis sample\n`sequencingType`|String|One of WG, EX or TS\n`reference`|String|Reference assembly id\n\n\n#### Optional workflow parameters:\nParameter|Value|Default|Description\n---|---|---|---\n`inputNormal`|File?|None|Optional input .bam file for control sample\n`bedgraphOutput`|Boolean|true|String that says TRUE or FALSE, determines if we need BedGraph output or not\n`outputFileNamePrefix`|String|\"\"|Prefix for outputs\n\n\n#### Optional task parameters:\nParameter|Value|Default|Description\n---|---|---|---\n`runFreec.intervalFile`|String?|None|Optional path to an interval .bed file, for targeted sequencing like EX, TS\n`runFreec.coefficientOfVariation`|Float|0.05|Parameter for CNV calling, default is 0.05\n`runFreec.breakPointThreshold`|Float|0.8|Parameter for CNV calling, default is 0.8\n`runFreec.contaminationAdjustment`|String?|None|informs FREEC about expected degree of contamination with normal tissue\n`runFreec.contaminationFraction`|Float|0.0|Contaminating fraction, by default is 0\n`runFreec.window`|Int|1000|Defines the resolution of the analysis, default:1000\n`runFreec.jobMemory`|Int|20|Memory in Gb for this job\n`runFreec.maxThreads`|Int|4|Maximum threads for the process, default is 4\n`runFreec.telocentromeric`|Int|50000|For human, we need 50000 (default)\n`runFreec.inputFormat`|String|\"BAM\"|Maybe SAM, BAM, pileup, bowtie, eland, arachne, psl (BLAT), BED. We use BAM\n`runFreec.mateOrientation`|String|\"FR\"|For paired-end Illumina we need FR, other types are also supported\n`runFreec.configFile`|String|\"config_freec.conf\"|config_freec.conf\n`runFreec.logPath`|String|\"freec_run.log\"|We have a log file which is not provisioned but can be examined if anything goes wrong\n`runFreec.timeout`|Int|72|Timeout in hours, needed to override imposed limits\n\n\n### Outputs\n\nOutput | Type | Description | Labels\n---|---|---|---\n`infoFile`|File|Info file for the calls|vidarr_label: infoFile\n`regionFile`|File|Region File|vidarr_label: regionFile\n`ratioFile`|File|Ratio File|vidarr_label: ratioFile\n`cnvTumor`|File|CNV for tumor file|vidarr_label: cnvTumor\n`cnvNormal`|File?|CNV for normal file|vidarr_label: cnvNormal\n`gcProfile`|File?|GC profile data|vidarr_label: gcProfile\n`ratioBedGraph`|File?|Retio BedGraph data|vidarr_label: ratioBedGraph\n\n\n## Commands\nThis section lists command(s) run by freec workflow\n \n* Running freec\n \nFREEC is a CNV-calling tool which may run in a control-free (Tumor-only) mode.\nThis workflow runs a custom python script which assembles a config file using\nthe provided inputs\n \n```\n  \n  Writing a config file given the inputs\n \n  ...\n \n  freec --conf iCONFIG_FILE \u003e\u003e LOG_PATH\n \n  ...\n \n  Post-processing and renaming of files\n \n```\n## Support\n\nFor support, please file an issue on the [Github project](https://github.com/oicr-gsi) or send an email to gsi@oicr.on.ca .\n\n_Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)_\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foicr-gsi%2Ffreec","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Foicr-gsi%2Ffreec","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Foicr-gsi%2Ffreec/lists"}