Wasted Compute

[PedalheadPHX]

When the sample was only sequenced on one lane this final merge is just reading and writing out the same file, could be a rename like in baserecalibration

phoenix/modules/dna_alignment/bwa_mem2_samtools.jst

Lines 264 to 276 in 9f04da2

	samtools merge \
	--threads 8 \
	-c \
	-f \
	-l 6 \
	"{{ temp_dir }}/{{ sample.name }}.bwa.md.bam" \
	{% for rgid in sample.read_groups %}
	{% if not loop.last %}
	"{{ temp_dir }}/{{ sample.name }}_{{ rgid }}.bwa.md.bam" \
	{% else %}
	"{{ temp_dir }}/{{ sample.name }}_{{ rgid }}.bwa.md.bam"
	{% endif %}
	{% endfor %}