CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
118 lines
3.4 KiB
Bash
Executable File
118 lines
3.4 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_tiny_fastq
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OUT="resources_test/$ID/"
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DIR="$OUT"
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# download cellranger tar gz
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cellranger_tar_gz="${OUT}/temp_cellranger-6.1.2.tar.gz"
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if [ ! -f "$cellranger_tar_gz" ]; then
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echo "Download Cell Ranger 6.1.2 manually first!"
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exit 1
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fi
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# untar fastqs
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cellranger_tiny_fastq="${OUT}/cellranger_tiny_fastq"
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if [ ! -f "${cellranger_tiny_fastq}/tinygex_S1_L001_R1_001.fastq.gz" ]; then
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mkdir -p "$cellranger_tiny_fastq"
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tar -xzf "$cellranger_tar_gz" \
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-C "$cellranger_tiny_fastq" \
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"cellranger-6.1.2/external/cellranger_tiny_fastq" \
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--strip-components=3
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fi
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# untar ref
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cellranger_tiny_ref="${OUT}/cellranger_tiny_ref"
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if [ ! -f "${cellranger_tiny_ref}/reference.json" ]; then
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mkdir -p "$cellranger_tiny_ref"
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tar -xzf "$cellranger_tar_gz" \
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-C "$cellranger_tiny_ref" \
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"cellranger-6.1.2/external/cellranger_tiny_ref" \
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--strip-components=3
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fi
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# Create ref with more recent STAR version
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recent_ref_dir="${OUT}/cellranger_tiny_ref_v2_7_10_a"
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if [ ! -f "${recent_ref_dir}/Genome" ]; then
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mkdir -p "${recent_ref_dir}"
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target/docker/mapping/star_build_reference/star_build_reference \
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--genome_fasta "$cellranger_tiny_ref/fasta/genome.fa" \
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--output "$recent_ref_dir" \
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--genomeSAindexNbases 7 \
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--transcriptome_gtf "$cellranger_tiny_ref/genes/genes.gtf.gz"
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fi
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# run cellranger count
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bam_dir="${OUT}/bam"
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if [ ! -f "$bam_dir/possorted_genome_bam.bam" ]; then
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mkdir -p "$bam_dir"
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viash run src/mapping/cellranger_count/config.vsh.yaml -- \
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--input "$cellranger_tiny_fastq" \
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--reference "$cellranger_tiny_ref" \
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--output "$bam_dir"
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fi
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# convert to h5mu
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raw_h5mu="${OUT}/raw_dataset.h5mu"
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if [ ! -f "$step1_h5mu" ]; then
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viash run src/convert/from_10xh5_to_h5mu/config.vsh.yaml -- \
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--input "${bam_dir}/raw_feature_bc_matrix.h5" \
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--output "$raw_h5mu"
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fi
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# run velocyto
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velo_gtf="$cellranger_tiny_ref/genes/genes.gtf.gz"
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velo_bam="$bam_dir/possorted_genome_bam.bam"
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velo_loom="${OUT}/velocyto.loom"
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if [ ! -f "$velo_loom" ]; then
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viash run src/velocity/velocyto/config.vsh.yaml -- \
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--input "$velo_bam" \
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--output "$velo_loom" \
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--transcriptome "$velo_gtf"
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fi
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# combine raw counts with velocyto data
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dataset_h5mu="${OUT}/dataset.h5mu"
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if [ ! -f "$dataset_h5mu" ]; then
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viash run src/velocity/velocyto_to_h5mu/config.vsh.yaml -- \
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--input_loom "$velo_loom" \
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--input_h5mu "$raw_h5mu" \
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--output "$dataset_h5mu"
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fi
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# run htseq
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htseq_counts="${OUT}/htseq_counts.tsv"
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if [ ! -f "$htseq_counts" ]; then
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viash run src/mapping/htseq_count/config.vsh.yaml -- \
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--input "$velo_bam" \
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--reference "$velo_gtf" \
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--output "$htseq_counts"
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fi
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multi_star="${OUT}/multi_star"
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if [ ! -d "$multi_star" ]; then
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viash run src/mapping/multi_star/config.vsh.yaml -- \
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--input_id "tinygex" \
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--input_r1 "$cellranger_tiny_fastq/tinygex_S1_L001_R1_001.fastq.gz" \
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--input_r2 "$cellranger_tiny_fastq/tinygex_S1_L001_R2_001.fastq.gz" \
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--input_id "tinygex" \
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--input_r1 "$cellranger_tiny_fastq/tinygex_S1_L002_R1_001.fastq.gz" \
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--input_r2 "$cellranger_tiny_fastq/tinygex_S1_L002_R2_001.fastq.gz" \
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--reference_index "$recent_ref_dir" \
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--reference_gtf "$cellranger_tiny_ref/genes/genes.gtf.gz" \
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--output "$multi_star" \
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---cpus 30
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fi |