Build branch openpipeline_spatial/h5mu-to-seurat with version h5mu-to-seurat to openpipeline_spatial on branch h5mu-to-seurat (3b5314b)

Build pipeline: test-vsh-ci-build-template-qlrkg

Source commit: 3b5314b60d

Source message: update changelog

resources_test_scripts/cosmx_tiny.sh

@@ -0,0 +1,52 @@
+#!/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"
+
+DIR="resources_test/cosmx"
+ID="Lung5_Rep2"
+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 "$OUT" ]; then
+    flat_dataset="https://nanostring-public-share.s3.us-west-2.amazonaws.com/SMI-Compressed/Lung5_Rep2/Lung5_Rep2+SMI+Flat+data.tar.gz"
+    wget  "$flat_dataset" -O "$TMPDIR/Lung5_Rep2.tar.gz"
+    mkdir -p "$TMPDIR/Lung5_Rep2"
+    tar -xzf "$TMPDIR/Lung5_Rep2.tar.gz" -C "$TMPDIR/Lung5_Rep2"
+    mkdir -p "$OUT"
+    mv "$TMPDIR/Lung5_Rep2/Lung5_Rep2/Lung5_Rep2-Flat_files_and_images/"* "$OUT/"
+fi
+
+viash run src/filter/subset_cosmx/config.vsh.yaml -- \
+    --input "$OUT" \
+    --num_fovs 3 \
+    --subset_transcripts_file True \
+    --subset_polygons_file False \
+    --output "${DIR}/${ID}_tiny"
+
+viash run src/convert/from_cosmx_to_h5mu/config.vsh.yaml -- \
+    --input ${DIR}/${ID}_tiny \
+    --output "$DIR/${ID}_tiny.h5mu" \
+    --output_compression "gzip"
+
+rm -rf "$OUT"
+
+# Sync to S3
+aws s3 sync \
+    --profile di \
+    "$DIR" \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/cosmx \
+    --delete \
+    --dryrun