#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    HCC1395_BL.bam##idx##HCC1395_BL.bai \
    1/HCC1395_BL.bam 2/HCC1395_BL.bam 3/HCC1395_BL.bam 4/HCC1395_BL.bam 5/HCC1395_BL.bam 6/HCC1395_BL.bam 7/HCC1395_BL.bam 8/HCC1395_BL.bam

# Touch index to ensure timestamp is newer than aligned file
touch HCC1395_BL.bai

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