#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    Filler-D0002474.bam##idx##Filler-D0002474.bai \
    1/Filler-D0002474.bam 2/Filler-D0002474.bam 3/Filler-D0002474.bam 4/Filler-D0002474.bam 5/Filler-D0002474.bam 6/Filler-D0002474.bam 7/Filler-D0002474.bam 8/Filler-D0002474.bam 9/Filler-D0002474.bam 10/Filler-D0002474.bam 11/Filler-D0002474.bam 12/Filler-D0002474.bam 13/Filler-D0002474.bam 14/Filler-D0002474.bam 15/Filler-D0002474.bam 16/Filler-D0002474.bam 17/Filler-D0002474.bam 18/Filler-D0002474.bam 19/Filler-D0002474.bam 20/Filler-D0002474.bam 21/Filler-D0002474.bam 22/Filler-D0002474.bam 23/Filler-D0002474.bam

# Touch index to ensure timestamp is newer than aligned file
touch Filler-D0002474.bai

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