sort_h2030

#!/bin/bash

configfile=server.conf

usage() { echo "Usage: $0 [-c <configfile>] <directories [...]>" 1>&2; exit $1; }

while getopts "c:h" o; do
	case "${o}" in
		c)	configfile=${OPTARG}
			if [[ ! -r ${configfile} ]]; then
				echo "Cannot read ${configfile}" 1>&2
				usage 2
			fi
			;;
		h)	usage 0	;;
		*)	usage 2	;;
	esac
done
shift $((OPTIND-1))

duplicates=1

. ${configfile}

: ${basedir:=$(pwd)}
: ${download:?}
: ${sampleset:?}



if (( ${#@} < 1)); then
	usage 2
fi

rx_runfold='^([[:digit:]]{2}[01][[:digit:]][0-3][[:digit:]])_([[:alnum:]]+)_([[:digit:]]+)_(0+-|[AB])([[:alnum:]]+)'  # e.g.: 200430_M01761_0414_000000000-J3JCT or 201023_A00730_0259_BHTVCCDRXX
#            ^-[1]: date                                     ^-[2]: instr   ^-[3]: run num ^-(prefix)^-[5]: flowcell

success=1
for d in "${@}"; do
	if [[ ! -d "${basedir}/${download}/${d}" ]]; then
		echo "No ${d}" 1>&2
		success=0
		continue
	fi
	csum=( "${basedir}/${download}/${d}/"*.check )
	if [[ "${csum[*]}" =~ [\*\[] ]]; then
		echo "No successful check sum in ${d}" 1>&2
		success=0
		continue
	fi

	#  552  2021-01-25 23:30:27 ./sort_samples_dumb -f sftp-health2030/210122_A00485_0093_BH2FM5DRXY/ -s '_H2FM5DRXY' -b 20210121_fused  -o sample-test/
	#  613  2021-01-29 16:42:24 ./sort_samples_dumb -f sftp-health2030/210128_A00485_0096_AH27VTDRXY/ -b 20210128_H27VTDRXY  -o sample-test/

	if [[ ${d} =~ ${rx_runfold} ]]; then
		flowcell="${BASH_REMATCH[5]}"
		batch="20${BASH_REMATCH[1]}_${flowcell}"
		quiet=''
		dupes=''
		if [[ -r "${sampleset}/samples.${batch}.tsv" ]]; then
			quiet='-q'
			echo "${batch} : ${d}"
		fi
		if (( duplicates )); then
			dupes='-D'
		fi
		./sort_samples_dumb ${quiet} ${dupes} -f ${basedir}/${download}/${d} -b "${batch}" -g -o "${sampleset}" ${mode:+-m ${mode}}|| success=0
		echo "type: h2030
lab: h2030
libkit: Illumina_COVIDSeq
fused: false
runfolder: ${d%%/}" > ${sampleset}/batch.${batch}.yaml

		echo -ne "\e[35;1m"
		(gawk '$3!=""{print;l=$3};$3==""{print $0 l;print "Sample "$1"-"$2" is empty">"/dev/stderr"}' ${sampleset}/samples.${batch}.tsv > ${sampleset}/samples.${batch}.tsv.patched) 2>&1
		echo -ne "\e[0m"
		mv ${sampleset}/samples.${batch}.tsv{.patched,}
	else
		echo "Can't parse ${d}"
	fi
done

if (( success )); then
	echo "All ok"
	exit 0
else
	echo "Some problems"
	exit 1
fi