#!/bin/bash -Ceuo pipefail
samtools \
    merge \
    -c \
    --threads 15 \
    --write-index \
     \
     \
    Sig_18_tissue.bam##idx##Sig_18_tissue.bai \
    1/Sig_18_tissue.bam 2/Sig_18_tissue.bam 3/Sig_18_tissue.bam 4/Sig_18_tissue.bam 5/Sig_18_tissue.bam 6/Sig_18_tissue.bam 7/Sig_18_tissue.bam 8/Sig_18_tissue.bam

# Touch index to ensure timestamp is newer than aligned file
touch Sig_18_tissue.bai

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