#!/bin/bash -Ceuo pipefail
samtools \
merge \
-c \
--threads 15 \
--write-index \
\
\
Sig_18_Blood.bam##idx##Sig_18_Blood.bai \
1/Sig_18_Blood.bam 2/Sig_18_Blood.bam 3/Sig_18_Blood.bam 4/Sig_18_Blood.bam 5/Sig_18_Blood.bam 6/Sig_18_Blood.bam 7/Sig_18_Blood.bam 8/Sig_18_Blood.bam
# Touch index to ensure timestamp is newer than aligned file
touch Sig_18_Blood.bai
cat <<-END_VERSIONS > versions.yml
"DAQ:SAMTOOLS_MERGE":
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS