#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    Filler-D0000539.bam##idx##Filler-D0000539.bai \
    1/Filler-D0000539.bam 2/Filler-D0000539.bam 3/Filler-D0000539.bam 4/Filler-D0000539.bam 5/Filler-D0000539.bam 6/Filler-D0000539.bam 7/Filler-D0000539.bam 8/Filler-D0000539.bam 9/Filler-D0000539.bam 10/Filler-D0000539.bam 11/Filler-D0000539.bam 12/Filler-D0000539.bam 13/Filler-D0000539.bam 14/Filler-D0000539.bam 15/Filler-D0000539.bam 16/Filler-D0000539.bam 17/Filler-D0000539.bam 18/Filler-D0000539.bam 19/Filler-D0000539.bam 20/Filler-D0000539.bam 21/Filler-D0000539.bam 22/Filler-D0000539.bam 23/Filler-D0000539.bam 24/Filler-D0000539.bam 25/Filler-D0000539.bam 26/Filler-D0000539.bam 27/Filler-D0000539.bam 28/Filler-D0000539.bam 29/Filler-D0000539.bam 30/Filler-D0000539.bam 31/Filler-D0000539.bam 32/Filler-D0000539.bam

# Touch index to ensure timestamp is newer than aligned file
touch Filler-D0000539.bai

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