CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
72 lines
2.1 KiB
Bash
Executable File
72 lines
2.1 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# TODO: we should turn this into viash components
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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=bdrhap_vdj
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OUT=resources_test/$ID
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n_threads=30
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# create raw directory
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raw_dir="$OUT/raw"
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mkdir -p "$raw_dir"
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# Check whether seqkit is available
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if ! command -v seqkit &> /dev/null; then
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echo "This script requires seqkit. Please make sure the binary is added to your PATH."
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exit 1
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fi
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# download and untar source fastq files
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tar_dir="$HOME/.cache/openpipeline/VDJDemo"
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if [[ ! -d "$tar_dir" ]]; then
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mkdir -p "$tar_dir"
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wget "http://bd-rhapsody-public.s3.amazonaws.com/Rhapsody-Demo-Data-Inputs/VDJDemo/VDJDemo.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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# subset fastq files
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for sample_id in RhapVDJDemo-BCR_S1_L001_R1_001 RhapVDJDemo-BCR_S1_L001_R2_001 RhapVDJDemo-mRNA_S5_L001_R1_001 RhapVDJDemo-mRNA_S5_L001_R2_001 RhapVDJDemo-TCR_S3_L001_R1_001 RhapVDJDemo-TCR_S3_L001_R2_001; do
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subset_file="$raw_dir/${sample_id}_subset.fastq.gz"
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if [[ ! -f "$subset_file" ]]; then
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echo "> Processing $sample_id"
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seqkit head -n 300000 "$tar_dir/$sample_id.fastq.gz" | gzip > "$subset_file"
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fi
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unset subset_file
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done
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# copy immune panel fasta
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fasta_file="$raw_dir/BD_Rhapsody_Immune_Response_Panel_Hs.fasta"
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if [[ ! -f "$fasta_file" ]]; then
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cp "$tar_dir/BD_Rhapsody_Immune_Response_Panel_Hs.fasta" "$fasta_file"
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fi
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# create params file
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cat > /tmp/params.yaml << HERE
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param_list:
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- id: "targeted_vdj"
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input: "$raw_dir/RhapVDJDemo-*_S*_L001_R[12]_001_subset.fastq.gz"
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mode: targeted
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reference: "$fasta_file"
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publish_dir: "$OUT/processed"
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putative_cell_call: "mRNA"
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vdj_version: human
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HERE
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# run bd rhapsody pipeline
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nextflow \
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run . \
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-main-script src/workflows/ingestion/bd_rhapsody/main.nf \
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-resume \
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-profile docker,mount_temp \
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-with-trace work/trace.txt \
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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 |