#!/bin/bash -euo pipefail
STAR-Fusion \
    --genome_lib_dir ctat_genome_lib_build_dir \
    --left_fq FFPE_HD789_01_RNA_13_A23YTGFLT4_1_1.fastp.fastq.gz --right_fq FFPE_HD789_01_RNA_13_A23YTGFLT4_1_2.fastp.fastq.gz \
    -J FFPE_HD789_01_RNA_13_A23YTGFLT4_1.Chimeric.out.junction \
    --CPU 4 \
    --examine_coding_effect \
    --output_dir . \
    --min_junction_reads 0 --min_sum_frags 1 --require_LDAS 0 --min_spanning_frags_only 1 --min_novel_junction_support 1 --examine_coding_effect --min_FFPM 0.00001

mv star-fusion.fusion_predictions.tsv FFPE_HD789_01_RNA_13_A23YTGFLT4_1.starfusion.starfusion.fusion_predictions.tsv
mv star-fusion.fusion_predictions.abridged.tsv FFPE_HD789_01_RNA_13_A23YTGFLT4_1.starfusion.starfusion.abridged.tsv
mv star-fusion.fusion_predictions.abridged.coding_effect.tsv FFPE_HD789_01_RNA_13_A23YTGFLT4_1.starfusion.starfusion.abridged.coding_effect.tsv

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:STARFUSION_WORKFLOW:STARFUSION":
    STAR-Fusion: $(STAR-Fusion --version 2>&1 | grep -i 'version' | sed 's/STAR-Fusion version: //')
END_VERSIONS