CI
5b8fa21d13
Build pipeline: openpipelines-bio.openpipeline.processing-workflows-quantijd49m
Source commit: 38f5f83d11
Source message: fix tests
73 lines
3.1 KiB
Bash
Executable File
73 lines
3.1 KiB
Bash
Executable File
#!/bin/bash
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# get the root of the directory
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REPO_ROOT=$(git rev-parse --show-toplevel)
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# ensure that the command below is run from the root of the repository
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cd "$REPO_ROOT"
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# The output folder
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OUT="resources_test/concat_test_data/"
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# create it if it doesn't exist already
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[ -d "$OUT" ] || mkdir -p "$OUT"
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echo "> Downloading files"
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target/docker/download/download_file/download_file \
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--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 \
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--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5"
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target/docker/download/download_file/download_file \
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--input https://cf.10xgenomics.com/samples/cell-arc/1.0.0/human_brain_3k/human_brain_3k_filtered_feature_bc_matrix.h5 \
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--output "${OUT}/human_brain_3k_filtered_feature_bc_matrix.h5"
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echo "> Converting to h5mu"
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viash run src/convert/from_10xh5_to_h5mu/config.vsh.yaml -- \
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--input "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5" \
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--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5mu"
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viash run src/convert/from_10xh5_to_h5mu/config.vsh.yaml -- \
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--input "$OUT/human_brain_3k_filtered_feature_bc_matrix.h5" \
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--output "$OUT/human_brain_3k_filtered_feature_bc_matrix.h5mu"
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echo "> Subsetting datasets"
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viash run src/filter/subset_h5mu/config.vsh.yaml -p docker -- \
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--input "$OUT/human_brain_3k_filtered_feature_bc_matrix.h5mu" \
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--output "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset.h5mu" \
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--number_of_observations 2000
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viash run src/filter/subset_h5mu/config.vsh.yaml -p docker -- \
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--input "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5mu" \
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--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset.h5mu" \
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--number_of_observations 2000
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echo "Making observation ids unique (required for concat component to function)"
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viash run src/metadata/add_id/config.vsh.yaml -- \
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--input "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset.h5mu" \
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--output "$OUT/human_brain_3k_filtered_feature_bc_matrix_subset_unique_obs.h5mu" \
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--input_id "human" \
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--make_observation_keys_unique
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viash run src/metadata/add_id/config.vsh.yaml -- \
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--input "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset.h5mu" \
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--output "$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset_unique_obs.h5mu" \
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--input_id "mouse" \
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--make_observation_keys_unique
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echo "Removing temp files"
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rm "${OUT}/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5mu" \
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"$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix.h5" \
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"$OUT/e18_mouse_brain_fresh_5k_filtered_feature_bc_matrix_subset.h5mu" \
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"$OUT/human_brain_3k_filtered_feature_bc_matrix_subset.h5mu" \
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"${OUT}/human_brain_3k_filtered_feature_bc_matrix.h5mu" \
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"$OUT/human_brain_3k_filtered_feature_bc_matrix.h5"
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echo "> Running concat component"
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viash run src/dataflow/concat/config.vsh.yaml -- \
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--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" \
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--input_id "human,mouse" \
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--output "$OUT/concatenated_brain_filtered_feature_bc_matrix_subset.h5mu"
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