modified ometiff_second_stitching.cwl and run_cytokit.cwl in steps folder #51
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running the entire pipeline (testing)
steps to setup environment:
conda create -n codex_pipeline python=3.9conda activate codex_pipelinegit clone https://github.com/hubmapconsortium/cwltool.gitcd cwltoolpip install .steps to run the pipeline:
cwltool --singularity --move-outputs --outdir /path/to/local/output/dir pipeline.cwl --data_dir (the path to the codex directory) --gpus '0,1'NOTE: This pipeline used lot of RAM (~200GB). 10 CPU's. It also requires GPU's