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poojachandra authored May 23, 2024
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# ichorCNA-wdl
WDL for https://github.com/GavinHaLab/ichorCNA. \
A revised version of [this WDL](https://github.com/GavinHaLab/wdl-repo/tree/main/ichorCNA/old/) so that it outputs plots.
[Here is info on a snakemake version](https://github.com/broadinstitute/ichorCNA/wiki/SnakeMake-pipeline-for-ichorCNA) for comparison.


The ichorCNA.wdl workflow has two tasks:
- `read_counter`
- `run_ichorCNA`
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- `~{sampleId}.RData`
- `~{sampleId}.plots.tar.gz`


## ichorCNA Wiki Page
For more info on the ichorCNA tool, visit the [Github Wiki page for ichorCNA](https://github.com/broadinstitute/ichorCNA/wiki) by the BROAD Institute.

## Configuration
### ichorCNA.wdl file
`taskDocker`: By default fredhutch/ichorcna:v0.5.0 is set, and doesn't need to be changed unless you wish to.\
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