CI
5b8fa21d13
Build pipeline: openpipelines-bio.openpipeline.processing-workflows-quantijd49m
Source commit: 38f5f83d11
Source message: fix tests
75 lines
2.1 KiB
Bash
Executable File
75 lines
2.1 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=$(git rev-parse --show-toplevel)
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# ensure that the command below is run from the root of the repository
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cd "$REPO_ROOT"
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# settings
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ID=cellranger_atac_tiny_bcl
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OUT="resources_test/$ID/"
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DIR="$OUT"
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REFERENCE_DIR=resources_test/reference_gencodev41_chr1
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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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viash ns build -q "download_file|cellranger_atac_mkfastq|build_cellranger_arc_reference|cellranger_atac_count" -p docker --setup cb
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# download bcl data
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if [ ! -f "${OUT}/bcl/sample_sheet.csv" ]; then
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mkdir -p "$OUT/bcl"
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# download tar gz
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target/docker/download/download_file/download_file \
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--input https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-1.0.0.tar.gz \
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--output "${OUT}/bcl/cellranger-atac-tiny-bcl-1.0.0.tar.gz"
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# untar
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tar -xf "${OUT}/bcl/cellranger-atac-tiny-bcl-1.0.0.tar.gz" \
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--strip-components=1 \
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-C "$OUT/bcl"
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# remove tar
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rm "${OUT}/bcl/cellranger-atac-tiny-bcl-1.0.0.tar.gz"
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# Download the layout file. It contains info about the samples (1 in this case) and lanes
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target/docker/download/download_file/download_file \
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--input https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-simple-1.0.0.csv \
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--output "${OUT}/bcl/layout.csv"
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# download sample sheet
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target/docker/download/download_file/download_file \
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--input https://cf.10xgenomics.com/supp/cell-atac/cellranger-atac-tiny-bcl-samplesheet-1.0.0.csv \
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--output "${OUT}/bcl/sample_sheet.csv"
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fi
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if [ ! -d "${OUT}/fastqs" ]; then
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mkdir -p "$OUT/fastqs"
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target/docker/demux/cellranger_atac_mkfastq/cellranger_atac_mkfastq \
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--input "${OUT}/bcl" \
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--csv "${OUT}/bcl/layout.csv" \
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--output "${OUT}/fastqs"
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fi
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# Create count matrices
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if [ ! -d "${OUT}/counts" ]; then
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mkdir -p "$OUT/counts"
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target/docker/mapping/cellranger_atac_count/cellranger_atac_count \
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--input "${OUT}/fastqs/HJN3KBCX2/test_sample/" \
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--reference "${REFERENCE_DIR}/reference_cellranger.tar.gz" \
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--output "${OUT}/counts"
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fi
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