Add script for cloud download of 2021Wu_human_breast_cancer_sc

Author: LouisK92

scripts/create_resources/process_wu_human_breast_cancer_sc.sh

@@ -0,0 +1,45 @@
+#!/bin/bash
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+set -e
+
+publish_dir="s3://openproblems-data/resources/datasets"
+
+# Note that the current download script and processing workflow have a specific default parameter set for the given dataset.
+# No additional datasets are supported by that component/workflow. Therefore the default parameters are used and don't need 
+# to be specified here.
+
+cat > /tmp/params.yaml << HERE
+param_list:
+  - id: wu_human_breast_cancer_sc/2021Wu_human_breast_cancer_sc
+    cancer_subtypes:
+      - HER2+
+      - TNBC
+      - ER+
+
+keep_files: false 
+
+output_dataset: "\$id/dataset.h5ad"
+output_meta: "\$id/dataset_meta.yaml"
+output_state: "\$id/state.yaml"
+publish_dir: "$publish_dir"
+HERE
+
+tw launch https://github.com/openproblems-bio/task_ist_preprocessing.git \
+  --revision build/main \
+  --pull-latest \
+  --main-script target/nextflow/datasets/workflows/process_wu_human_breast_cancer_sc/main.nf \
+  --workspace 53907369739130 \
+  --compute-env 6TeIFgV5OY4pJCk8I0bfOh \
+  --params-file /tmp/params.yaml \
+  --config common/nextflow_helpers/labels_tw.config \
+  --labels datasets,wu_human_breast_cancer_sc
+
+aws s3 sync \
+  s3://openproblems-data/resources/datasets/wu_human_breast_cancer_sc/2021Wu_human_breast_cancer_sc \
+  resources/datasets/wu_human_breast_cancer_sc/2021Wu_human_breast_cancer_sc