CI
fd31f6f50d
Build pipeline: openpipelines-bio.openpipeline-spatial.v0.3.0-t5q65
Source commit: 84e2b7cc63
Source message: update version
60 lines
2.5 KiB
Bash
Executable File
60 lines
2.5 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=$(git rev-parse --show-toplevel)
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# Define absolute directory path
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DIR="$REPO_ROOT/resources_test/visium"
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ID="Visium_FFPE_Human_Ovarian_Cancer_tiny"
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# from https://www.10xgenomics.com/resources/datasets/human-ovarian-cancer-1-standard
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mkdir -p "$DIR"
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# Input Files - download to the specific directory
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curl -o "$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
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curl -o "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" https://cf.10xgenomics.com/samples/spatial-exp/1.3.0/Visium_FFPE_Human_Ovarian_Cancer/Visium_FFPE_Human_Ovarian_Cancer_image.jpg
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curl -o "$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
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# Extract in the specific directory
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tar xvf "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs.tar" -C "$DIR"
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# Create subsampled dataset with ImageMagick
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# https://imagemagick.org/index.php
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mkdir -p "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny"
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convert "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg" -resize 2000x2000 "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image_tiny.jpg"
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for f in "$DIR"/Visium_FFPE_Human_Ovarian_Cancer_fastqs/*L001*R*; do
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gzip -cdf "$f" | head -n 40000 | gzip -c > "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny/$(basename "$f")";
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done
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echo "> Downloading and subsampling of datasets complete"
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# Run spaceranger
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viash run src/mapping/spaceranger_count/config.vsh.yaml -- \
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--input "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny" \
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--gex_reference "$REPO_ROOT/resources_test/GRCh38/" \
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--probe_set "$DIR/Visium_FFPE_Human_Ovarian_Cancer_probe_set.csv" \
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--image "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image_tiny.jpg" \
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--slide "V10L13-020" \
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--area "D1" \
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--create_bam "false" \
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--output "Visium_FFPE_Human_Ovarian_Cancer_tiny_spaceranger"
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mv
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echo "> Running spaceranger complete"
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rm -rf "$DIR/Visium_FFPE_Human_Ovarian_Cancer_fastqs"
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rm -f "$DIR/Visium_FFPE_Human_Ovarian_Cancer_image.jpg"
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viash run "$REPO_ROOT/src/convert/from_spaceranger_to_h5mu/config.vsh.yaml" -- \
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--input "$DIR/Visium_FFPE_Human_Ovarian_Cancer_tiny_spaceranger" \
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--output "$DIR/$ID.h5mu"
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aws s3 sync \
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--profile di \
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--exclude "*.yaml" \
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"$DIR" \
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s3://openpipelines-bio/openpipeline_spatial/resources_test/visium \
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--delete \
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--dryrun |