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/visium_tiny.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+
+set -eo pipefail
+
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# Define absolute directory path
+DIR="$REPO_ROOT/resources_test/visium"
+
+# from https://www.10xgenomics.com/resources/datasets/human-ovarian-cancer-1-standard
+mkdir -p "$DIR"
+
+# Input Files - download to the specific directory
+curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar
+curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_image.jpg
+curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv
+
+# Extract in the specific directory
+tar xvf "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" -C "$DIR"
+
+# Create subsampled dataset with ImageMagick
+# https://imagemagick.org/index.php
+mkdir -p "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny"
+convert "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" -resize 2000x2000 "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image_tiny.jpg"
+for f in "$DIR"/Visium_FFPE_Human_Ovarian_Cancer_fastqs/*L001*R*; do 
+  gzip -cdf "$f" | head -n 40000 | gzip -c > "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny/$(basename "$f")"; 
+done
+
+echo "> Downloading and subsampling of datasets complete"
+
+# Run spaceranger
+viash run src/mapping/spaceranger_count/config.vsh.yaml -- \
+  --input "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny" \
+  --gex_reference "$REPO_ROOT/resources_test/GRCh38/" \
+  --probe_set "$DIR/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv" \
+  --image "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image_tiny.jpg" \
+  --slide "V10L13-020" \
+  --area "D1" \
+  --create_bam "false" \
+  --output "Visium_FFPE_Human_Ovarian_Cancer_tiny_spaceranger"
+
+mv 
+echo "> Running spaceranger complete"
+
+rm -rf "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs"
+rm -f "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg"
+
+aws s3 sync \
+    --profile di \
+    --exclude "*.yaml" \
+    "$DIR" \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/visium \
+    --delete \
+    --dryrun