CI
5b8fa21d13
Build pipeline: openpipelines-bio.openpipeline.processing-workflows-quantijd49m
Source commit: 38f5f83d11
Source message: fix tests
60 lines
2.0 KiB
Bash
Executable File
60 lines
2.0 KiB
Bash
Executable File
#!/bin/bash
|
|
|
|
# ensure that the command below is run from the root of the repository
|
|
REPO_ROOT=$(git rev-parse --show-toplevel)
|
|
cd "$REPO_ROOT"
|
|
|
|
# settings
|
|
ID=rna_velocity
|
|
OUT=resources_test/$ID
|
|
|
|
|
|
# create raw directory
|
|
velocyto_dir="$OUT/velocyto"
|
|
mkdir -p "$velocyto_dir"
|
|
|
|
########################################################
|
|
# Create a compatible BAM file from BD Rhapsody Output #
|
|
########################################################
|
|
|
|
bd_rhap_wta_bam="resources_test/bdrhap_5kjrt/processed/output_raw/Combined_sample_Bioproduct.bam"
|
|
|
|
if [[ ! -f "$bd_rhap_wta_bam" ]]; then
|
|
echo "$bd_rhap_wta_bam does not exist. Please generate BD Rhapsody test data first."
|
|
exit 1
|
|
fi
|
|
|
|
echo "> Converting BD Rhapsody barcode tags."
|
|
viash run src/convert/from_bd_to_10x_molecular_barcode_tags/config.vsh.yaml -- \
|
|
-i "$bd_rhap_wta_bam" \
|
|
-o "$velocyto_dir/compatible_bd_input.bam" \
|
|
--bam \
|
|
-t 4
|
|
|
|
echo "> Creating barcodes file."
|
|
samtools view -@4 "$velocyto_dir/compatible_bd_input.bam" | \
|
|
grep -oP "(?<=CB:Z:)\S+" | sort | uniq | head > "$velocyto_dir/barcodes.txt"
|
|
|
|
###########################################################
|
|
# Process Tiny Fast Fastq dataset from 10X to create #
|
|
# input data for convert/from_velocyto_to_h5mu compontent #
|
|
###########################################################
|
|
|
|
mkdir "$OUT/velocyto_processed"
|
|
|
|
gtf="resources_test/cellranger_tiny_fastq/cellranger_tiny_ref/genes/genes.gtf.gz"
|
|
bam="resources_test/cellranger_tiny_fastq/bam/possorted_genome_bam.bam"
|
|
|
|
echo "> Processing 10x dataset"
|
|
viash run src/velocity/velocyto/config.vsh.yaml -- \
|
|
-i "$bam" \
|
|
-o "$OUT/velocyto_processed/cellranger_tiny.loom" \
|
|
--transcriptome "$gtf"
|
|
|
|
echo "> Converting loom file to MuData object"
|
|
viash run src/velocity/velocyto_to_h5mu/config.vsh.yaml -- \
|
|
--input_loom "$OUT/velocyto_processed/cellranger_tiny.loom" \
|
|
--input_h5mu "resources_test/cellranger_tiny_fastq/raw_dataset.h5mu" \
|
|
--modality velocyto \
|
|
--output_compression "gzip" \
|
|
--output "$OUT/velocyto_processed/velocyto.h5mu" |