#!/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 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2 \
    --abundance 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2/abundance.tsv \
    --output_qc 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.sample_qc.tsv \
    --output_scores 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.sample_scores.tsv \
    --output_gene_table 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.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