CI
1683fce826
Build pipeline: vsh-ci-build-template-pn6wx
Source commit: e92e56b491
Source message: Merge remote-tracking branch 'origin/main' into v3.0
203 lines
6.0 KiB
Bash
Executable File
203 lines
6.0 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_anticmv
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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 "$raw_dir"
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# Check whether seqkit is available
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if ! command -v seqkit &> /dev/null; then
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echo "This script requires seqkit. Please make sure the binary is added to your PATH."
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exit 1
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fi
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# dataset page:
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# https://www.10xgenomics.com/resources/datasets/integrated-gex-totalseqc-and-tcr-analysis-of-connect-generated-library-from-5k-cmv-t-cells-2-standard
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# check whether reference is available
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reference_dir="resources_test/reference_gencodev41_chr1/"
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genome_tar="$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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# download and untar source fastq files
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tar_dir="$HOME/.cache/openpipeline/5k_human_antiCMV_T_TBNK_connect_Multiplex"
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if [[ ! -d "$tar_dir" ]]; then
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mkdir -p "$tar_dir"
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# download fastqs and untar
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wget "https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-vdj/6.1.2/5k_human_antiCMV_T_TBNK_connect_Multiplex/5k_human_antiCMV_T_TBNK_connect_Multiplex_fastqs.tar" -O "$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 > "$output"
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fi
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}
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orig_sample_id="5k_human_antiCMV_T_TBNK_connect"
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seqkit_head "$tar_dir/gex_1/${orig_sample_id}_GEX_1_S1_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_GEX_1_subset_S1_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/gex_1/${orig_sample_id}_GEX_1_S1_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_GEX_1_subset_S1_L001_R2_001.fastq.gz"
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seqkit_head "$tar_dir/ab/${orig_sample_id}_AB_S2_L004_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_AB_subset_S2_L004_R1_001.fastq.gz"
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seqkit_head "$tar_dir/ab/${orig_sample_id}_AB_S2_L004_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_AB_subset_S2_L004_R2_001.fastq.gz"
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seqkit_head "$tar_dir/vdj/${orig_sample_id}_VDJ_S1_L001_R1_001.fastq.gz" "$raw_dir/${orig_sample_id}_VDJ_subset_S1_L001_R1_001.fastq.gz"
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seqkit_head "$tar_dir/vdj/${orig_sample_id}_VDJ_S1_L001_R2_001.fastq.gz" "$raw_dir/${orig_sample_id}_VDJ_subset_S1_L001_R2_001.fastq.gz"
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# download immune panel fasta if needed
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feature_reference="$raw_dir/feature_reference.csv"
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if [[ ! -f "$feature_reference" ]]; then
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wget "https://cf.10xgenomics.com/samples/cell-vdj/6.1.2/5k_human_antiCMV_T_TBNK_connect_Multiplex/5k_human_antiCMV_T_TBNK_connect_Multiplex_count_feature_reference.csv" -O "$feature_reference"
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fi
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# download vdj reference if needed
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vdj_ref="$raw_dir/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0.tar.gz"
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if [[ ! -f "$vdj_ref" ]]; then
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wget "https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0.tar.gz" -O "$vdj_ref"
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fi
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# Run mapping pipeline
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cat > /tmp/params.yaml << HERE
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param_list:
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- id: "$ID"
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input: "$raw_dir"
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library_id:
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- "${orig_sample_id}_GEX_1_subset"
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- "${orig_sample_id}_AB_subset"
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- "${orig_sample_id}_VDJ_subset"
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library_type:
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- "Gene Expression"
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- "Antibody Capture"
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- "VDJ"
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gex_reference: "$genome_tar"
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vdj_reference: "$vdj_ref"
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feature_reference: "$feature_reference"
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publish_dir: "$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.config \
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-c src/workflows/utils/errorstrat_ignore.config
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# Convert to h5mu
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cat > /tmp/params.yaml << HERE
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id: "$orig_sample_id"
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input: "$OUT/processed/10x_5k_anticmv.cellranger_multi.output"
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publish_dir: "$OUT/"
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output: "*.h5mu"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/convert/from_cellranger_multi_to_h5mu/main.nf \
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-resume \
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-profile docker,mount_temp \
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-params-file /tmp/params.yaml \
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-c src/workflows/utils/labels.config
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mv "$OUT/0.h5mu" "$OUT/${orig_sample_id}.h5mu"
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# run qc workflow
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cat > /tmp/params.yaml << HERE
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id: "$ID"
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input: "$OUT/$orig_sample_id.h5mu"
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var_name_mitochondrial_genes: mitochondrial
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var_name_ribosomal_genes: ribosomal
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publish_dir: "$OUT/"
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output: "${orig_sample_id}_qc.h5mu"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/workflows/qc/qc/main.nf \
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-resume \
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-profile docker,mount_temp \
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-params-file /tmp/params.yaml \
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-c src/workflows/utils/labels.config
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# Run full pipeline
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cat > /tmp/params.yaml << HERE
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id: "$ID"
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input: "$OUT/${orig_sample_id}_qc.h5mu"
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publish_dir: "$OUT/"
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output: "${orig_sample_id}_mms.h5mu"
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HERE
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nextflow \
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run . \
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-main-script target/nextflow/workflows/multiomics/process_samples/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.config
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# create fastqc directory
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fastqc_dir="$OUT/fastqc"
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mkdir -p "$fastqc_dir"
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./target/executable/qc/fastqc/fastqc \
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--input "$raw_dir" \
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--mode "dir" \
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--output "$fastqc_dir"
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# Create a test dataset for the Custom modality
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# by just labeling the AB as custom
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feat_ref_name=$(basename $feature_reference)
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sed -e 's/Antibody Capture/Custom/g' "$feature_reference" > "/tmp/custom_${feat_ref_name}"
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cat > /tmp/params_custom.yaml << HERE
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param_list:
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- id: "$ID"
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input: "$raw_dir"
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library_id:
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- "${orig_sample_id}_GEX_1_subset"
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- "${orig_sample_id}_AB_subset"
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- "${orig_sample_id}_VDJ_subset"
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library_type:
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- "Gene Expression"
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- "Custom"
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- "VDJ"
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gex_reference: "$genome_tar"
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feature_reference: "/tmp/custom_${feat_ref_name}"
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vdj_reference: "$vdj_ref"
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publish_dir: "$OUT/processed_with_custom"
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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_custom.yaml \
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-c src/workflows/utils/labels.config \
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-c src/workflows/utils/errorstrat_ignore.config |