#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    NTC_0002_0013_B23KGCJLT4_1.bam##idx##NTC_0002_0013_B23KGCJLT4_1.bai \
    1/NTC_0002_0013_B23KGCJLT4_1.bam 2/NTC_0002_0013_B23KGCJLT4_1.bam 3/NTC_0002_0013_B23KGCJLT4_1.bam 4/NTC_0002_0013_B23KGCJLT4_1.bam 5/NTC_0002_0013_B23KGCJLT4_1.bam 6/NTC_0002_0013_B23KGCJLT4_1.bam 7/NTC_0002_0013_B23KGCJLT4_1.bam 8/NTC_0002_0013_B23KGCJLT4_1.bam

# Touch index to ensure timestamp is newer than aligned file
touch NTC_0002_0013_B23KGCJLT4_1.bai

cat <<-END_VERSIONS > versions.yml
"DAQ:SAMTOOLS_MERGE":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS