#!/bin/bash -Ceuo pipefail
set -euo pipefail
export JAVA_TOOL_OPTIONS='-Xmx8g -XX:+UseParallelGC'
PicardCommandLine MarkDuplicates \
    I='two.sorted.bam' \
    O='two.markdup.bam' \
    M='two.markdup_metrics.txt' \
    TMP_DIR="$PWD" \
    VALIDATION_STRINGENCY=SILENT \
    MAX_RECORDS_IN_RAM=250000 \
    REMOVE_DUPLICATES=false \
    CREATE_INDEX=true \
    TAG_DUPLICATE_SET_MEMBERS=true \
    TAGGING_POLICY=All \
    OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500
# Picard/htsjdk may write <rg>.markdup.bai; we standardize on <rg>.markdup.bam.bai for Nextflow outputs
if [[ -f 'two.markdup.bam.bai' ]]; then
    :
elif [[ -f 'two.markdup.bai' ]]; then
    ln -sf 'two.markdup.bai' 'two.markdup.bam.bai'
else
    echo "MarkDuplicates did not create 'two.markdup.bam.bai' or 'two.markdup.bai'" >&2
    exit 1
fi