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Build branch build/main with version build_main (491efce)

Browse Source 
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-kj8js

Source commit: 491efceaaf

Source message: deploy: 7f820d2607f3e1fabc0183915d1bb427715e18ae
This commit is contained in:
CI
2025-07-10 12:45:04 +00:00
parent 4d10ea15db
commit 096d01f274
31 changed files with 7789 additions and 27 deletions
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19
resources_test_scripts/reference_tiny.sh Executable file
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@@ -0,0 +1,19 @@
#!/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/GRCh38"
mkdir -p $DIR
aws s3 sync \
--profile di \
s3://openpipelines-bio/openpipeline_spatial/resources_test/GRCh38 \
"$DIR" \
--delete \
--dryrun

35
resources_test_scripts/visium_tiny.sh Normal file
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@@ -0,0 +1,35 @@
#!/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 "$DIR/subsampled"
convert "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" -resize 2000x2000 "$DIR/subsampled/Visium_FFPE_Human_Ovarian_Cancer_image.jpg"
for f in "$DIR"/Visium_FFPE_Human_Ovarian_Cancer_fastqs/*L001*R*; do
gzip -cdf "$f" | head -n 40000 | gzip -c > "$DIR/subsampled/$(basename "$f")";
done
aws s3 sync \
--profile di \
"$DIR" \
s3://openpipelines-bio/openpipeline_spatial/resources_test/visium \
--delete \
--dryrun

12
resources_test_scripts/xenium_tiny.sh
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@@ -5,12 +5,10 @@ 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/xenium/"
# Define absolute directory paths
DIR="$REPO_ROOT/resources_test/xenium"
ID="xenium_tiny"
OUT="$DIR/$ID/"
OUT="$DIR/$ID"
# create tempdir
MY_TEMP="${VIASH_TEMP:-/tmp}"
@@ -29,11 +27,11 @@ if [ ! -d "$OUT" ]; then
mv "$TMPDIR/xenium_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs/"* "$OUT/"
fi
viash run src/convert/from_xenium_to_spatialdata/config.vsh.yaml -- \
viash run "$REPO_ROOT/src/convert/from_xenium_to_spatialdata/config.vsh.yaml" -- \
--input "$OUT" \
--output "$DIR/$ID.zarr"
viash run src/convert/from_spatialdata_to_h5mu/config.vsh.yaml -- \
viash run "$REPO_ROOT/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml" -- \
--input "$DIR/$ID.zarr" \
--output "$DIR/$ID.h5mu"