Issue filtering host with >2 read files

[LanderDC]

Hi,

When I try to filter my reads (3 files) against my host genome without the quality filter (has already been performed beforehand), I get an error from minimap2:

[ERROR] incorrect input: in the sr mode, please specify no more than two query files.

I believe the issue is on these lines:

EsViritu/src/EsViritu/EsViritu_general.sh

Lines 156 to 157 in 6b2df8f

	minimap2 -t $CPUS -ax sr ${FILTER_LOC}/filter_seqs.fna ${READS} | \
	samtools fastq -n -f 4 - > ${TEMP_DIR}/${SAMPLE}.EV_input.fastq

and can be fixed by:

cat ${READS} | minimap2 -t $CPUS -ax sr ${FILTER_LOC}/filter_seqs.fna - | \
samtools fastq -n -f 4 - > ${TEMP_DIR}/${SAMPLE}.EV_input.fastq

Thanks!