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Build branch openpipeline/processing-workflows-quantile-filtering with version processing-workflows-quantile-filtering to openpipeline on branch processing-workflows-quantile-filtering (38f5f83d)

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Build pipeline: openpipelines-bio.openpipeline.processing-workflows-quantijd49m

Source commit: 38f5f83d11

Source message: fix tests
This commit is contained in:
CI
2026-06-09 18:32:44 +00:00
commit 5b8fa21d13
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resources_test_scripts/concat_test_data.sh Executable file
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#!/bin/bash
# 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"
# The output folder
OUT="resources_test/concat_test_data/"
# create it if it doesn't exist already
[ -d "$OUT" ] || mkdir -p "$OUT"
echo "> Downloading files"
target/docker/download/download_file/download_file \
--input https://cf.10xgenomics.com/samples/cell-arc/1.0.0/e18_mouse_brain_fresh_5k/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5 \
--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5"
target/docker/download/download_file/download_file \
--input https://cf.10xgenomics.com/samples/cell-arc/1.0.0/human_brain_3k/human_brain_3k_filtered_feature_bc_matrix.h5 \
--output "${OUT}/human_brain_3k_filtered_feature_bc_matrix.h5"
echo "> Converting to h5mu"
viash run src/convert/from_10xh5_to_h5mu/config.vsh.yaml -- \
--input "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5" \
--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5mu"
viash run src/convert/from_10xh5_to_h5mu/config.vsh.yaml -- \
--input "$OUT/human_brain_3k_filtered_feature_bc_matrix.h5" \
--output "$OUT/human_brain_3k_filtered_feature_bc_matrix.h5mu"
echo "> Subsetting datasets"
viash run src/filter/subset_h5mu/config.vsh.yaml -p docker -- \
--input "$OUT/human_brain_3k_filtered_feature_bc_matrix.h5mu" \
--output "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset.h5mu" \
--number_of_observations 2000
viash run src/filter/subset_h5mu/config.vsh.yaml -p docker -- \
--input "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5mu" \
--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset.h5mu" \
--number_of_observations 2000
echo "Making observation ids unique (required for concat component to function)"
viash run src/metadata/add_id/config.vsh.yaml -- \
--input "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset.h5mu" \
--output "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu" \
--input_id "human" \
--make_observation_keys_unique
viash run src/metadata/add_id/config.vsh.yaml -- \
--input "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset.h5mu" \
--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu" \
--input_id "mouse" \
--make_observation_keys_unique
echo "Removing temp files"
rm "${OUT}/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5mu" \
"$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5" \
"$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset.h5mu" \
"$OUT/human_brain_3k_filtered_feature_bc_matrix_subset.h5mu" \
"${OUT}/human_brain_3k_filtered_feature_bc_matrix.h5mu" \
"$OUT/human_brain_3k_filtered_feature_bc_matrix.h5"
echo "> Running concat component"
viash run src/dataflow/concat/config.vsh.yaml -- \
--input "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu,$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu" \
--input_id "human,mouse" \
--output "$OUT/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"