#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam##idx##1136_27F-T1-TDNA-1_A23MHWWLT4_1.bai \
    1/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 2/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 3/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 4/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 5/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 6/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 7/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 8/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 9/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 10/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 11/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 12/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 13/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 14/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 15/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 16/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 17/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 18/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 19/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 20/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 21/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 22/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 23/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 24/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 25/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 26/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 27/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 28/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 29/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 30/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 31/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam 32/1136_27F-T1-TDNA-1_A23MHWWLT4_1.bam

# Touch index to ensure timestamp is newer than aligned file
touch 1136_27F-T1-TDNA-1_A23MHWWLT4_1.bai

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