CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
55 lines
1.7 KiB
Bash
Executable File
55 lines
1.7 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=rna_velocity
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OUT=resources_test/$ID
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# create raw directory
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velocyto_dir="$OUT/velocyto"
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mkdir -p "$velocyto_dir"
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########################################################
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# Create a compatible BAM file from BD Rhapsody Output #
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########################################################
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bd_rhap_wta_bam="resources_test/bdrhap_5kjrt/processed/WTA.bd_rhapsody.output_raw/sample_final.BAM"
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if [[ ! -f "$bd_rhap_wta_bam" ]]; then
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echo "$bd_rhap_wta_bam does not exist. Please generate BD Rhapsody test data first."
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exit 1
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fi
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echo "> Converting BD Rhapsody barcode tags."
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viash run src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml -- \
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-i "$bd_rhap_wta_bam" \
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-o "$velocyto_dir/compatible_bd_input.bam" \
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--bam \
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-t 4
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echo "> Creating barcodes file."
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samtools view -@4 "$velocyto_dir/compatible_bd_input.bam" | \
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grep -oP "(?<=CB:Z:)\S+" | sort | uniq | head > "$velocyto_dir/barcodes.txt"
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###########################################################
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# Process Tiny Fast Fastq dataset from 10X to create #
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# input data for convert/from_velocyto_to_h5mu compontent #
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###########################################################
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mkdir "$OUT/velocyto_processed"
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gtf="resources_test/cellranger_tiny_fastq/cellranger_tiny_ref/genes/genes.gtf.gz"
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bam="resources_test/cellranger_tiny_fastq/bam/possorted_genome_bam.bam"
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echo "> Processing 10x dataset"
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viash run src/velocity/velocyto/config.vsh.yaml -- \
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-i "$bam" \
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-o "$OUT/velocyto_processed/cellranger_tiny.loom" \
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--transcriptome "$gtf"
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