diff --git a/WDL/README.md b/WDL/README.md index edfc923..4e8ab22 100644 --- a/WDL/README.md +++ b/WDL/README.md @@ -18,7 +18,7 @@ The workflow outputs 8 files: ## Configuration ### ichorCNA.wdl file -`taskDocker`: By default the WDL pipeline is curently usiing this [docker image] (gavinhalab/ichorcna:0.0.1) +`taskDocker`: By default the WDL pipeline is curently using this `gavinhalab/ichorcna:0.0.1` `taskCPU`: CPU variable for run_ichorCNA. May have to edit `read_counter` CPU in its runtime section. `memory`: This may have to be edited in both `read_counter` and `run_ichorCNA` in their runtime sections. @@ -68,11 +68,13 @@ Workflow level params ## Outputs A complete list of outputs can be found in [this Github wiki page](https://github.com/broadinstitute/ichorCNA/wiki/Output) along with parameter info. -## Instructions -1) To run WDL on your machine, first you need to install [cromwell](https://github.com/broadinstitute/cromwell/releases/tag/85) or run it in a workspace that had Cromwell server configured already. -2) The `inputs.json` file currently is created for one sample. To create one `inputs.json` file for multiple samples run: +## Instructions to setup WDL Pipeline +1) Pull the docker image using : + `docker pull mskilab/jabba:1.0.0` +2) To run WDL on your machine, first you need to install [cromwell](https://github.com/broadinstitute/cromwell/releases/tag/85) or run it in a workspace thathas Cromwell server configured already. +3) The `inputs.json` file currently is created for one sample. To create one `inputs.json` file for multiple samples run: - python3 create_input_json.py input_test_ichorCNA.csv inputs.json + `python3 create_input_json.py input_test_ichorCNA.csv inputs.json` This command creates a json file with all the samples present in the input `input_test_ichorCNA.csv` . Please check the format of the csv file.