CI
1683fce826
Build pipeline: vsh-ci-build-template-pn6wx
Source commit: e92e56b491
Source message: Merge remote-tracking branch 'origin/main' into v3.0
127 lines
4.2 KiB
Bash
Executable File
127 lines
4.2 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# ensure that the command below is run from the root of the repository
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REPO_ROOT=$(git rev-parse --show-toplevel)
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cd "$REPO_ROOT"
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# settings
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ID=10x_5k_beam
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OUT="resources_test/$ID"
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# create raw directory
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raw_dir="$OUT/raw"
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mkdir -p "$raw_dir"
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# Check whether seqkit is available
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if ! command -v seqkit &> /dev/null; then
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echo "This script requires seqkit. Please make sure the binary is added to your PATH."
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exit 1
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fi
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# check whether reference is available
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reference_dir="resources_test/reference_gencodev41_chr1/"
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genome_tar="$reference_dir/reference_cellranger.tar.gz"
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if [[ ! -f "$genome_tar" ]]; then
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echo "$genome_tar does not exist. Please create the reference genome first"
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exit 1
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fi
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# dataset page:
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# https://www.10xgenomics.com/datasets/5k-human-a0201-b0702-pbmcs-beam-t-2-standard
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# download and untar source fastq files
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tar_dir="$HOME/.cache/openpipeline/5k_human_A0201_B0702_PBMCs_BEAM_T"
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if [[ ! -d "$tar_dir" ]]; then
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mkdir -p "$tar_dir"
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# download fastqs and untar
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wget "https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_fastqs.tar" -O "$tar_dir.tar"
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tar -xvf "$tar_dir.tar" -C "$tar_dir" --strip-components=1
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rm "$tar_dir.tar"
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fi
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function seqkit_head {
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input="$1"
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output="$2"
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if [[ ! -f "$output" ]]; then
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echo "> Processing `basename $input`"
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seqkit head -n 200000 "$input" | gzip > "$output"
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fi
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}
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orig_sample_id="beamt_human_A0201_B0702_pbmc"
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seqkit_head "$tar_dir/gex/${orig_sample_id}_gex_S3_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_gex_subset_S3_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/gex/${orig_sample_id}_gex_S3_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_gex_subset_S3_L001_R2_001.fastq.gz"
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seqkit_head "$tar_dir/vdj/${orig_sample_id}_vdj_S2_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_vdj_subset_S2_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/vdj/${orig_sample_id}_vdj_S2_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_vdj_subset_S2_L001_R2_001.fastq.gz"
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seqkit_head "$tar_dir/antigen_capture/${orig_sample_id}_ag_S1_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_ag_subset_S1_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/antigen_capture/${orig_sample_id}_ag_S1_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_ag_subset_S1_L001_R2_001.fastq.gz"
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# download feature reference
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feature_ref="$raw_dir/beamt_human_A0201_B0702_pbmc_feature_reference.csv"
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if [[ ! -f "$feature_ref" ]]; then
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wget "https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_count_feature_reference.csv" -O "$feature_ref"
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fi
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# download vdj reference if needed
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vdj_ref="$raw_dir/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_vdj_reference.tar.gz"
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if [[ ! -f "$vdj_ref" ]]; then
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wget "https://cf.10xgenomics.com/samples/cell-vdj/7.1.0/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex/5k_BEAM-T_Human_A0201_B0702_PBMC_5pv2_Multiplex_vdj_reference.tar.gz" -O "$vdj_ref"
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fi
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# Run mapping pipeline
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# TODO: Also include conversion to h5mu
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cat > /tmp/params.yaml << HERE
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param_list:
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- id: "$ID"
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input: "$raw_dir"
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library_id:
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- "${orig_sample_id}_gex_subset"
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- "${orig_sample_id}_vdj_subset"
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- "${orig_sample_id}_ag_subset"
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library_type:
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- "Gene Expression"
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- "VDJ-T"
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- "Antigen Capture"
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gex_reference: "$genome_tar"
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feature_reference: "$feature_ref"
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vdj_reference: "$vdj_ref"
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control_id:
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- negative_control_A0201
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- negative_control_B0702
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mhc_allele:
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- "HLA-A*02:01"
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- "HLA-B*07:02"
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publish_dir: "$OUT/processed"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/mapping/cellranger_multi/main.nf \
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-resume \
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-profile docker,mount_temp \
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-params-file /tmp/params.yaml \
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-c src/workflows/utils/labels_ci.config
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# Create h5mu
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cat > /tmp/params.yaml << HERE
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id: "$ID"
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input: "$OUT/processed/$ID.cellranger_multi.output"
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publish_dir: "$OUT/"
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output: "$orig_sample_id.h5mu"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
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-resume \
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-profile docker,mount_temp \
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-params-file /tmp/params.yaml \
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-c src/workflows/utils/labels_ci.config
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