consensus_qc task not compatible with lowercase seqs in FASTAs

[kapsakcj]

When you have a nucleotide fasta that is all lowercase:

>fasta-header
atacgagcgcgagcgcgcacnnnacncnancgcgattg.......

The task & workflow (TheiaCov_FASTA and others) completes successfully, but results in all 0s for output metrics: numberN, number ATCG, number_Degenerate, number_Total, percent_reference_coverage

Adding the -i case insensitive flag with grep -i [...] should resolve this and/or perhaps add other lower case letters in grep -E "C|c|A|a|T|t|G|g"

public_health_viral_genomics/tasks/task_qc_utils.wdl

Lines 181 to 202 in acdbc23

	command <<<
	# capture date and version
	date | tee DATE
	num_N=$( grep -v ">" ~{assembly_fasta} | grep -o 'N' | wc -l )
	if [ -z "$num_N" ] ; then num_N="0" ; fi
	echo $num_N | tee NUM_N
	num_ACTG=$( grep -v ">" ~{assembly_fasta} | grep -o -E "C|A|T|G" | wc -l )
	if [ -z "$num_ACTG" ] ; then num_ACTG="0" ; fi
	echo $num_ACTG | tee NUM_ACTG
	# calculate percent coverage (Wu Han-1 genome length: 29903bp)
	python3 -c "print ( round( ($num_ACTG / 29903 ) * 100, 2 ) )" | tee PERCENT_REF_COVERAGE
	num_degenerate=$( grep -v ">" ~{assembly_fasta} | grep -o -E "B|D|E|F|H|I|J|K|L|M|O|P|Q|R|S|U|V|W|X|Y|Z" | wc -l )
	if [ -z "$num_degenerate" ] ; then num_degenerate="0" ; fi
	echo $num_degenerate | tee NUM_DEGENERATE
	num_total=$( grep -v ">" ~{assembly_fasta} | grep -o -E '[A-Z]' | wc -l )
	if [ -z "$num_total" ] ; then num_total="0" ; fi
	echo $num_total | tee NUM_TOTAL