diff --git a/app/raw_analysis/CELLRANGER_MULTI_template_v1.txt b/app/raw_analysis/CELLRANGER_MULTI_template_v1.txt index d01db65..cb1b7e4 100644 --- a/app/raw_analysis/CELLRANGER_MULTI_template_v1.txt +++ b/app/raw_analysis/CELLRANGER_MULTI_template_v1.txt @@ -36,7 +36,9 @@ analysis_metadata: - "#sample_id,cmo_ids,description" - "#[samples] # for Fixed RNA Profiling multiplexed libraries only" - "#sample_id,probe_barcode_ids,description" - scanpy: + scanpy_config: + TEMPLATE_FILE: /project/tgu/software/scanpy-notebook-image/templates/scanpy_single_sample_analysis_v0.0.6.3.ipynb + IMAGE_FILE: /project/tgu/resources/pipeline_resource/singularity_images/scanpy-notebook-image/scanpy-notebook-image_v0.0.4.sif MITO_PREFIX: MT- RUN_SCRUBLET: true RUN_CELLCYCLE_SCORE: true