#!/bin/bash -euo pipefail
expression_qc_and_signatures.py \
    --signatures_master signatures_master.json \
    --tx2gene Homo_sapiens.GRCh38.102.tx2gene_full.tsv \
    --target_panel twist_rna_exome_target_regions_hg38_annotated.bed \
    --sample_id FFPE_V4_0002_RNA_0001_B23MVV7LT4_1 \
    --abundance FFPE_V4_0002_RNA_0001_B23MVV7LT4_1/abundance.tsv \
    --output_qc FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.sample_qc.tsv \
    --output_scores FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.sample_scores.tsv \
    --output_gene_table FFPE_V4_0002_RNA_0001_B23MVV7LT4_1.gene_table.tsv \


cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:KALLISTO_TO_TX2GENE_QC":
    python: $(python3 --version | sed 's/Python //g')
    expression_qc_and_signatures: 1.0.0
END_VERSIONS