CI
cd5554d22f
Build pipeline: vsh-ci-build-template-k4qzr
Source commit: 173327cc56
Source message: Cellranger multi conversion: fix combined AB + CB probe experiments (#1062)
119 lines
3.7 KiB
Bash
Executable File
119 lines
3.7 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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ID=pbmc_1k_protein_v3
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OUT=resources_test/$ID/$ID
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DIR=$(dirname "$OUT")
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# ideally, this would be a versioned pipeline run
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[ -d "$DIR" ] || mkdir -p "$DIR"
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# dataset page:
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# https://www.10xgenomics.com/resources/datasets/1-k-pbm-cs-from-a-healthy-donor-gene-expression-and-cell-surface-protein-3-standard-3-0-0
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# download metrics summary
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wget https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_metrics_summary.csv \
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-O "${OUT}_metrics_summary.csv"
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# download counts h5 file
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wget https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5 \
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-O "${OUT}_filtered_feature_bc_matrix.h5"
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wget https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_raw_feature_bc_matrix.h5 \
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-O "${OUT}_raw_feature_bc_matrix.h5"
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# download counts matrix tar gz file
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wget https://cf.10xgenomics.com/samples/cell-exp/3.0.0/pbmc_1k_protein_v3/pbmc_1k_protein_v3_filtered_feature_bc_matrix.tar.gz \
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-O "${OUT}_filtered_feature_bc_matrix.tar.gz"
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# extract matrix tar gz
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mkdir -p "${OUT}_filtered_feature_bc_matrix"
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tar -xvf "${OUT}_filtered_feature_bc_matrix.tar.gz" \
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-C "${OUT}_filtered_feature_bc_matrix" \
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--strip-components 1
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rm "${OUT}_filtered_feature_bc_matrix.tar.gz"
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# convert 10x h5 to h5mu
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target/docker/convert/from_10xh5_to_h5mu/from_10xh5_to_h5mu \
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--input "${OUT}_filtered_feature_bc_matrix.h5" \
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--input_metrics_summary "${OUT}_metrics_summary.csv" \
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--output "${OUT}_filtered_feature_bc_matrix.h5mu"
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# run single sample
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nextflow \
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run . \
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-main-script target/nextflow/workflows/rna/rna_singlesample/main.nf \
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-c src/workflows/utils/labels_ci.config \
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-profile docker \
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--id pbmc_1k_protein_v3_uss \
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--input "${OUT}_filtered_feature_bc_matrix.h5mu" \
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--output "`basename $OUT`_uss.h5mu" \
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--publishDir `dirname $OUT` \
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-resume
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# add the sample ID to the mudata object
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nextflow \
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run . \
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-main-script target/nextflow/metadata/add_id/main.nf \
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-c src/workflows/utils/labels_ci.config \
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-profile docker \
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--id pbmc_1k_protein_v3_uss \
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--input "${OUT}_uss.h5mu" \
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--input_id "pbmc_1k_protein_v3_uss" \
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--output "`basename $OUT`_uss_with_id.h5mu" \
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--output_compression "gzip" \
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--publishDir `dirname $OUT` \
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-resume
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# run multisample
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nextflow \
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run . \
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-main-script target/nextflow/workflows/rna/rna_multisample/main.nf \
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-c src/workflows/utils/labels_ci.config \
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-profile docker \
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--id pbmc_1k_protein_v3_ums \
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--input "${OUT}_uss_with_id.h5mu" \
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--output "`basename $OUT`_ums.h5mu" \
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--publishDir `dirname $OUT` \
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-resume
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rm "${OUT}_uss_with_id.h5mu"
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# run dimred
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nextflow \
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run . \
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-main-script target/nextflow/workflows/multiomics/dimensionality_reduction/main.nf \
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-c src/workflows/utils/labels_ci.config \
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-profile docker \
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--id pbmc_1k_protein_v3_mms \
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--input "${OUT}_ums.h5mu" \
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--output "`basename $OUT`_mms.h5mu" \
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--publishDir `dirname $OUT` \
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--obs_covariates sample_id \
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-resume
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# run integration
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nextflow \
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run . \
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-main-script target/nextflow/workflows/integration/harmony_leiden/main.nf \
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-c src/workflows/utils/labels_ci.config \
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-profile docker \
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--id pbmc_1k_protein_v3_mms_integration \
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--input "${OUT}_mms.h5mu" \
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--output "`basename $OUT`_mms.h5mu" \
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--publishDir `dirname $OUT` \
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--obs_covariates sample_id \
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-resume
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python <<HEREDOC
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import mudata as mu
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mudata = mu.read_h5mu("${DIR}/pbmc_1k_protein_v3_filtered_feature_bc_matrix.h5mu")
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mudata.mod["rna"].write_h5ad("${DIR}/pbmc_1k_protein_v3_filtered_feature_bc_matrix_rna.h5ad")
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HEREDOC |