#!/bin/bash -Ceuo pipefail
samtools \
merge \
-c \
--threads 15 \
--write-index \
\
\
Filler-D0002881.bam##idx##Filler-D0002881.bai \
1/Filler-D0002881.bam 2/Filler-D0002881.bam 3/Filler-D0002881.bam 4/Filler-D0002881.bam 5/Filler-D0002881.bam 6/Filler-D0002881.bam 7/Filler-D0002881.bam 8/Filler-D0002881.bam
# Touch index to ensure timestamp is newer than aligned file
touch Filler-D0002881.bai
cat <<-END_VERSIONS > versions.yml
"DAQ:SAMTOOLS_MERGE":
samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS