From 9e3fa86302386f8770b8abdf84e5fbf75092143c Mon Sep 17 00:00:00 2001
From: V-Z <vojta@trapa.cz>
Date: Wed, 6 Dec 2017 14:11:28 +0100
Subject: [PATCH] Fixed problem with output file path of FLASh.

---
 sondovac_part_a.sh | 9 +++++++--
 sondovac_part_b.sh | 3 +++
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/sondovac_part_a.sh b/sondovac_part_a.sh
index 5aeda14..412ed9f 100755
--- a/sondovac_part_a.sh
+++ b/sondovac_part_a.sh
@@ -222,6 +222,9 @@ workdirpath
 
 # Check availability of all needed binaries
 
+# Check if realpath is available
+checktools realpath
+
 # Check if paste is available
 checktools paste
 
@@ -1145,11 +1148,13 @@ if [[ -n "$REFERENCEMT" && -n "$REFERENCEMT0" ]]; then
 	echo
 
 	# Combine the paired-end reads with FLASH - with mitochondrial reads
+	# Sanitize output variable for usage by FLASh (it always starts with './', thus absolute URL is not usable)
+	FLASHOUT2=$(realpath --relative-to=$WORKDIR $FLASHOUT)
 	echo "${REDF}Step 4 of the pipeline${NORM} - combination of paired-end reads."
 	echo
 	echo "${CYAF}Combining paired-end reads${NORM}"
 	echo
-	flash -o $FLASHOUT -M $FLASHM $FASTQNOMT.1.fq $FASTQNOMT.2.fq || {
+	flash -o $FLASHOUT2 -M $FLASHM $FASTQNOMT.1.fq $FASTQNOMT.2.fq || {
 		echo
 		echo "${REDF}${BOLD}Error!${NORM} ${CYAF}Combining paired-end reads failed.${NORM} Aborting. Check if files"
 		echo "${REDF}$REFERENCEMT${NORM}, ${REDF}$FASTQNOMT.1.fq${NORM} and ${REDF}$FASTQNOMT.2.fq${NORM} are correct."
@@ -1163,7 +1168,7 @@ if [[ -n "$REFERENCEMT" && -n "$REFERENCEMT0" ]]; then
 		echo
 		echo "${CYAF}Combining paired-end reads${NORM}"
 		echo
-		flash -o $FLASHOUT -M $FLASHM `echo $FASTQNOCP`_1.fq `echo $FASTQNOCP`_2.fq || {
+		flash -o $FLASHOUT2 -M $FLASHM `echo $FASTQNOCP`_1.fq `echo $FASTQNOCP`_2.fq || {
 			echo
 			echo "${REDF}${BOLD}Error!${NORM} ${CYAF}Combining paired-end reads failed.${NORM} Aborting. Check if files"
 			echo "${REDF}$REFERENCECP${NORM}, ${REDF}`echo $FASTQNOCP`_1.fq${NORM} and ${REDF}`echo $FASTQNOCP`_2.fq${NORM} are correct."
diff --git a/sondovac_part_b.sh b/sondovac_part_b.sh
index c8c4489..a381c34 100755
--- a/sondovac_part_b.sh
+++ b/sondovac_part_b.sh
@@ -226,6 +226,9 @@ workdirpath
 
 # Check availability of all needed binaries
 
+# Check if realpath is available
+checktools realpath
+
 # Check if grep is available
 checktools grep