#!/bin/bash -Ceuo pipefail
N7_analysis.R \
    --sample-id "HCC1395_tumor_vs_HCC1395_BL" \
    --cnv-segments "HCC1395_tumor_vs_HCC1395_BL.segments.csv" \
    --somatic-vcf "HCC1395_tumor_vs_HCC1395_BL.vcf.gz" \
    --cn-signatures "COSMIC_v3.5_CN_GRCh37.txt" \
    --sbs-signatures "COSMIC_v3.5_SBS_GRCh38.txt" \
    --indel-signatures "COSMIC_v3.5_ID_GRCh37.txt" \
    --output-dir "." \
    --model tso_fit_cla.v02.rds \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:N7_COSMIC_SIGS":
    n7_cosmic_sigs: 0.0.1
    r-base: $(Rscript -e 'cat(as.character(getRversion()))' 2>/dev/null || echo "4.3.3")
END_VERSIONS