#!/bin/bash -Ceuo pipefail
predict.py \
    --vcf       659_bhK-T1-TDNA-1_B23KFCWLT4_1_vs_659_bhK-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.annotated.vcf.gz \
    --model     model.pkl \
    --pon-dir   pon \
    --cosmic    cosmic_fusion.tsv.gz \
    --genes     protein_coding_genes.bed \
    --panel-bed foresight_panel_for_manta.bed \
    --prefix    659_bhK-T1-TDNA-1_B23KFCWLT4_1_vs_659_bhK-N1-BDNA-1_B23KGCJLT4_1.manta_fusion \
    --threshold 0.05 \
    --tumor-id  "659_bhK-T1-TDNA-1_B23KFCWLT4_1" \
    --normal-id "659_bhK-N1-BDNA-1_B23KGCJLT4_1"

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_SCORE":
    python: $( python3 --version 2>&1 | sed 's/Python //' )
    lightgbm: $( python3 -c "import lightgbm; print(lightgbm.__version__)" )
    scikit-learn: $( python3 -c "import sklearn; print(sklearn.__version__)" )
    predict_py: "1.3.0"
END_VERSIONS