CI
1581a62139
Build pipeline: openpipelines-bio.openpipeline-spatial.v0.2.0-bgdj2
Source commit: 327d79399b
Source message: Merge remote-tracking branch 'origin/main' into v0.2
44 lines
1.2 KiB
Bash
Executable File
44 lines
1.2 KiB
Bash
Executable File
#!/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 "$OUT" ]; then
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tiny_dataset="https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip"
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wget "$tiny_dataset" -O "$TMPDIR/xenium_tiny.zip"
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unzip -q "$TMPDIR/xenium_tiny.zip" -d "$TMPDIR/xenium_tiny"
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mkdir -p "$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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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/$ID.h5mu"
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# Sync to S3
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aws s3 sync \
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--profile di \
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"$DIR" \
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s3://openpipelines-bio/openpipeline_spatial/resources_test/xenium \
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--delete \
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--dryrun |