Build branch openpipeline_spatial/update-mudata with version update-mudata to openpipeline_spatial on branch update-mudata (2f79910)

Build pipeline: openpipelines-bio.openpipeline-spatial.update-mudata-pssvw

Source commit: 2f7991091d

Source message: linting

resources_test_scripts/xenium_tiny.sh

@@ -0,0 +1,44 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# Define absolute directory paths
+DIR="$REPO_ROOT/resources_test/xenium"
+ID="xenium_tiny"
+OUT="$DIR/$ID"
+
+# create tempdir
+MY_TEMP="${VIASH_TEMP:-/tmp}"
+TMPDIR=$(mktemp -d "$MY_TEMP/$ID-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+if [ ! -d "$OUT" ]; then
+    tiny_dataset="https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip"
+    wget "$tiny_dataset" -O "$TMPDIR/xenium_tiny.zip"
+
+    unzip -q "$TMPDIR/xenium_tiny.zip" -d "$TMPDIR/xenium_tiny"
+    mkdir -p "$OUT"
+    mv "$TMPDIR/xenium_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs/"* "$OUT/"
+fi
+
+viash run "$REPO_ROOT/src/convert/from_xenium_to_spatialdata/config.vsh.yaml" -- \
+    --input "$OUT" \
+    --output "$DIR/$ID.zarr"
+
+viash run "$REPO_ROOT/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml" -- \
+    --input "$DIR/$ID.zarr" \
+    --output "$DIR/$ID.h5mu"
+
+# Sync to S3
+aws s3 sync \
+    --profile di \
+    "$DIR" \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/xenium \
+    --delete \
+    --dryrun