Build branch fix-integration-tests with version dev (2dbe3b72)

Build pipeline: vsh-ci-dev-k8tz4

Source commit: 2dbe3b7231

Source message: Fix pointers to test resources

resources_test_scripts/hlca_reference_model.sh

@@ -0,0 +1,58 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# 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"
+
+ID=HLCA_reference_model
+OUT=resources_test/$ID/$ID
+DIR=$(dirname "$OUT")
+
+# ideally, this would be a versioned pipeline run
+[ -d "$DIR" ] || mkdir -p "$DIR"
+
+# download and unarchive pre-trained scANVI model
+wget https://zenodo.org/record/6337966/files/HLCA_reference_model.zip \
+  -O "${OUT}.zip"
+
+# # Test query data
+# # Source publication: Delorey, Toni M., et al. “COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.” Nature 595.7865 (2021): 107-113.
+# wget https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5230nnn/GSM5230027/suppl/GSM5230027_04-P103142-S149-R01_raw_feature_bc_matrix.h5.gz \
+#   -O "${OUT}_query_test.h5.gz"
+# gzip -d "${OUT}_query_test.h5.gz"
+
+# # Prepare test data as in scvi-tools tutorial: https://docs.scvi-tools.org/en/stable/tutorials/notebooks/query_hlca_knn.html
+# python <<HEREDOC
+# import pandas as pd
+# import scanpy as sc
+
+# geo_metadata_url = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE171nnn/GSE171668/suppl/GSE171668_lung_metadata.csv.gz"
+# metadata = pd.read_csv(geo_metadata_url, index_col=0)
+
+# DATA_PATH = "${OUT}_query_test.h5"
+# query_data = sc.read_10x_h5(DATA_PATH)
+# # clean up .var.index (gene names)
+# query_data.var['gene_names'] = query_data.var.index
+# query_data.var.index = [idx.split("___")[-1] for idx in query_data.var.gene_ids]
+# # clean up cell barcodes:
+# query_data.obs.index = query_data.obs.index.str.rstrip("-1")
+# # read in metadata (to select only cells of interest and remove empty drops)
+# # subset to cells from our sample
+# metadata = metadata.loc[metadata.donor == "D12_4",:].copy()
+# # clean up barcodes:
+# metadata.index = [idx.split("-")[-1] for idx in metadata.index]
+# # subset adata to cells in metadata:
+# query_data = query_data[metadata.index,:].copy()
+# # add dataset information:
+# query_data.obs['dataset'] = "test_dataset_delorey_regev"
+# sc.write(DATA_PATH, query_data)
+# HEREDOC
+
+# # convert 10x h5 to h5mu
+# viash run src/convert/from_h5ad_to_h5mu/config.vsh.yaml -- \
+#   --input "${OUT}_query_test.h5" \
+#   --output "${OUT}_query_test.h5mu"