Build branch openpipeline_spatial/v0.4 with version v0.4.0 to openpipeline_spatial on branch v0.4 (e41c3a4)

Build pipeline: openpipelines-bio.openpipeline-spatial.v0.4.0-2g7tn

Source commit: e41c3a485f

Source message: update version

resources_test_scripts/xenium_tiny.sh

@@ -0,0 +1,109 @@
+#!/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 "$OUT" ]; then
+    tiny_dataset="https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.tar.gz"
+    wget "$tiny_dataset" -O "$TMPDIR/xenium_tiny.tar.gz"
+
+    mkdir -p "$TMPDIR/xenium_tiny"
+    tar -xzf "$TMPDIR/xenium_tiny.tar.gz" -C "$TMPDIR/xenium_tiny"
+    mkdir -p "$OUT"
+    mv "$TMPDIR/xenium_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs/"* "$OUT/"
+fi
+
+rm -rf "$DIR/$ID.zarr"
+viash run "$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"
+
+cat > /tmp/qc.yaml <<EOF
+param_list:
+  - id: xenium_tiny
+    input: "$DIR/$ID.h5mu"
+var_name_mitochondrial_genes: mitochondrial
+var_name_ribosomal_genes: ribosomal
+output: '\$id.qc.h5mu'
+output_compression: gzip
+publish_dir: "$DIR"
+EOF
+
+nextflow run openpipelines-bio/openpipeline \
+  -latest \
+  -r 2.1.0 \
+  -main-script target/nextflow/workflows/qc/qc/main.nf \
+  -profile docker \
+  -params-file /tmp/qc.yaml \
+  -resume \
+  -config src/workflows/utils/labels_ci.config
+
+viash run "$REPO_ROOT/src/neighbors/spatial_neighborhood_graph/config.vsh.yaml" -- \
+    --input "$DIR/$ID.qc.h5mu" \
+    --output "$DIR/${ID}.qc.neighbors.h5mu"
+
+cat > /tmp/pca.yaml <<EOF
+param_list:
+  - id: xenium_tiny
+    input: "$DIR/${ID}.qc.neighbors.h5mu"
+output: '\$id.qc.neighbors.pca.h5mu'
+output_compression: gzip
+publish_dir: "$TMPDIR"
+EOF
+
+nextflow run openpipelines-bio/openpipeline \
+  -latest \
+  -r v4.0.3 \
+  -main-script target/nextflow/dimred/pca/main.nf \
+  -profile docker \
+  -params-file /tmp/pca.yaml \
+  -config src/workflows/utils/labels_ci.config \
+  -resume
+
+cat > /tmp/find_neighbors.yaml <<EOF
+param_list:
+  - id: xenium_tiny
+    input: "$TMPDIR/xenium_tiny.qc.neighbors.pca.h5mu"
+output: '\$id.qc.all_neighbors.pca.h5mu'
+output_compression: gzip
+publish_dir: "$TMPDIR"
+EOF
+
+nextflow run openpipelines-bio/openpipeline \
+  -latest \
+  -r v4.0.3 \
+  -main-script target/nextflow/neighbors/find_neighbors/main.nf \
+  -profile docker \
+  -params-file /tmp/find_neighbors.yaml \
+  -config src/workflows/utils/labels_ci.config \
+  -resume
+
+# Move the final output to the destination directory
+mv "$TMPDIR/xenium_tiny.qc.all_neighbors.pca.h5mu" "$DIR/xenium_tiny.qc.all_neighbors.pca.h5mu"
+
+# Sync to S3
+aws s3 sync \
+    --profile di \
+    "$DIR" \
+    s3://openpipelines-bio/openpipeline_spatial/resources_test/xenium \
+    --delete \
+    --dryrun