#!/bin/bash -euo pipefail
printf 'sample_name,vaf_p90,is_contaminated,contamination_pct\n' > "SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.predictions.csv"
printf '%s,,skipped,0\n' 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1' >> "SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1.predictions.csv"

{
    echo "#id: 'rna_contamination'"
    echo "#plot_type: 'generalstats'"
    echo "#pconfig:"
    echo "#    is_contaminated:"
    echo "#        namespace: 'RNA contamination'"
    echo "#        title: 'RNA contaminated'"
    echo "#        description: 'Whether the sample was classified as contaminated from VAF_p90'"
    echo "#    contamination_pct:"
    echo "#        namespace: 'RNA contamination'"
    echo "#        title: 'RNA contamination %'"
    echo "#        description: 'Estimated RNA contamination from VAF_p90; 0% for samples classified as clean'"
    echo "#        format: '{:,.2f}'"
    echo "#        suffix: '%'"
    printf '%s\t%s\t%s\n' 'Sample' 'is_contaminated' 'contamination_pct'
    printf "'%s'\tSkipped\tN/A\n" 'SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1'
} > "SkinN_FFPE_L01_RNA_01_B23LG7FLT4_1_contamination_mqc.tsv"

printf '%s\n' '"NFCORE_RNAFUSION:RNAFUSION:CONTAMINATION_SKIPPED_LOW_READS":' > versions.yml
printf '%s\n' '    contamination_skipped_low_reads: 1.0.0' >> versions.yml