109 lines
2.9 KiB
Bash
109 lines
2.9 KiB
Bash
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#!/bin/bash
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set -eo pipefail
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# get the root of the directory
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REPO_ROOT=$(git rev-parse --show-toplevel)
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# Define absolute directory paths
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DIR="$REPO_ROOT/resources_test/xenium"
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ID="xenium_tiny"
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OUT="$DIR/$ID"
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# create tempdir
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MY_TEMP="${VIASH_TEMP:-/tmp}"
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TMPDIR=$(mktemp -d "$MY_TEMP/$ID-XXXXXX")
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function clean_up {
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[[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
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}
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trap clean_up EXIT
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if [ ! -d "$OUT" ]; then
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tiny_dataset="https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.tar.gz"
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wget "$tiny_dataset" -O "$TMPDIR/xenium_tiny.tar.gz"
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mkdir -p "$TMPDIR/xenium_tiny"
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tar -xzf "$TMPDIR/xenium_tiny.tar.gz" -C "$TMPDIR/xenium_tiny"
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mkdir -p "$OUT"
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mv "$TMPDIR/xenium_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs/"* "$OUT/"
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fi
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rm -rf "$DIR/$ID.zarr"
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viash run "$REPO_ROOT/src/convert/from_xenium_to_spatialdata/config.vsh.yaml" -- \
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--input "$OUT" \
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--output "$DIR/$ID.zarr"
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viash run "$REPO_ROOT/src/convert/from_spatialdata_to_h5mu/config.vsh.yaml" -- \
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--input "$DIR/$ID.zarr" \
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--output "$DIR/$ID.h5mu"
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cat > /tmp/qc.yaml <<EOF
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param_list:
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- id: xenium_tiny
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input: "$DIR/$ID.h5mu"
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var_name_mitochondrial_genes: mitochondrial
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var_name_ribosomal_genes: ribosomal
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output: '\$id.qc.h5mu'
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output_compression: gzip
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publish_dir: "$DIR"
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EOF
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nextflow run openpipelines-bio/openpipeline \
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-latest \
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-r 2.1.0 \
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-main-script target/nextflow/workflows/qc/qc/main.nf \
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-profile docker \
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-params-file /tmp/qc.yaml \
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-resume \
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-config src/workflows/utils/labels_ci.config
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viash run "$REPO_ROOT/src/neighbors/spatial_neighborhood_graph/config.vsh.yaml" -- \
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--input "$DIR/$ID.qc.h5mu" \
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--output "$DIR/${ID}.qc.neighbors.h5mu"
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cat > /tmp/pca.yaml <<EOF
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param_list:
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- id: xenium_tiny
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input: "$DIR/${ID}.qc.neighbors.h5mu"
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output: '\$id.qc.neighbors.pca.h5mu'
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output_compression: gzip
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publish_dir: "$TMPDIR"
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EOF
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nextflow run openpipelines-bio/openpipeline \
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-latest \
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-r v4.0.3 \
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-main-script target/nextflow/dimred/pca/main.nf \
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-profile docker \
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-params-file /tmp/pca.yaml \
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-config src/workflows/utils/labels_ci.config \
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-resume
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cat > /tmp/find_neighbors.yaml <<EOF
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param_list:
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- id: xenium_tiny
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input: "$TMPDIR/xenium_tiny.qc.neighbors.pca.h5mu"
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output: '\$id.qc.all_neighbors.pca.h5mu'
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output_compression: gzip
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publish_dir: "$TMPDIR"
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EOF
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nextflow run openpipelines-bio/openpipeline \
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-latest \
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-r v4.0.3 \
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-main-script target/nextflow/neighbors/find_neighbors/main.nf \
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-profile docker \
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-params-file /tmp/find_neighbors.yaml \
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-config src/workflows/utils/labels_ci.config \
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-resume
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# Move the final output to the destination directory
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mv "$TMPDIR/xenium_tiny.qc.all_neighbors.pca.h5mu" "$DIR/xenium_tiny.qc.all_neighbors.pca.h5mu"
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# Sync to S3
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aws s3 sync \
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--profile di \
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"$DIR" \
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s3://openpipelines-bio/openpipeline_spatial/resources_test/xenium \
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--delete \
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--dryrun
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