#!/bin/bash -Ceuo pipefail
# Use local filesystem for cnvkit's temporary files to avoid filesystem consistency issues on networked filesystems
export TMPDIR=/var/tmp
mkdir -p $TMPDIR


    samtools index HCC1395_BL.recalibrated.bam
samtools index HCC1395_tumor.recalibrated.bam


cnvkit.py \
    batch \
    HCC1395_tumor.recalibrated.bam \
    --normal HCC1395_BL.recalibrated.bam \
    --fasta Homo_sapiens_assembly38.fasta \
     \
    --targets xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21.bed \
    --processes 8 \
    --method hybrid --diagram --scatter

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_CNVKIT:CNVKIT_BATCH":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
    cnvkit: $(cnvkit.py version | sed -e 's/cnvkit v//g')
END_VERSIONS