#!/bin/bash -Ceuo pipefail
analyze \
    --tumor-bam HCC1395_tumor.recalibrated.bam \
    --normal-bam normal/HCC1395_BL.recalibrated.bam \
    --case-id HCC1395_tumor_vs_HCC1395_BL \
    --save \
    --save-location . \
    --save-format both \
    --name HCC1395_tumor_vs_HCC1395_BL \
    --cores 16 \
    --coverage 100 \
    --confidence-interval 0.95 \
     --microsatellites-list 1500_dropped_panel_with_boosted_msi_regions.tsv --model mi_msi_v0_4_0_200x_attn.model --use-attention 

mimsi_results_to_json.py HCC1395_tumor_vs_HCC1395_BL_results.txt HCC1395_tumor_vs_HCC1395_BL_results.json

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MIMSI_ANALYZE":
    mimsi: $(analyze --version 2>&1 | sed 's/.*version - //; s/ .*//' || echo 'unknown')
END_VERSIONS