From bd56cb059f49dc0c027c3790e8c9f51c12393f5e Mon Sep 17 00:00:00 2001
From: Peter Belmann <pbelmann@cebitec.uni-bielefeld.de>
Date: Sun, 12 May 2024 07:57:47 +0000
Subject: [PATCH] fix(emgb): add titles mount

---
 bin/emgb.sh | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/bin/emgb.sh b/bin/emgb.sh
index aad1dc23..1c766797 100755
--- a/bin/emgb.sh
+++ b/bin/emgb.sh
@@ -19,6 +19,8 @@ while [ $# -gt 0 ]; do
 	    ;;
             --type=*) TYPE="${1#*=}"
 	    ;;
+            --titles=*) TITLES="${1#*=}"
+	    ;;
 	    --blastdb=*) BLAST_DB="${1#*=}"
 	    ;;
 	    --version) VERSION_CHECK=1
@@ -40,7 +42,7 @@ done
 
 
 function getGenes {
-	nr=$(find $OUTPUT_PATH/$RUN_ID/annotation/ -name "*.${BLAST_DB}.blast.tsv" -exec readlink -f {} \;  | sed 's/^/ -nr-blast-tab /g')
+	nr=$(find $OUTPUT_PATH/$RUN_ID/annotation/ -name "*.${BLAST_DB}.blast.tsv" -exec readlink -f {} \;  | sed 's/^/ --blast-tab /g')
 	tax=$(find $OUTPUT_PATH/$RUN_ID/annotation/ -name "*.taxonomy.tsv" -exec readlink -f {} \; | sed 's/^/ -mmseqs-lineage /g')
 	ffn=$(find $OUTPUT_PATH/$RUN_ID/annotation -name "*.ffn.gz" -exec readlink -f {} \; | sed 's/^/ -ffn /g')
 	gff=$(find $OUTPUT_PATH/$RUN_ID/annotation -name "*.gff.gz" -exec readlink -f {} \; | sed 's/^/ -gff /g')
@@ -50,14 +52,22 @@ function getGenes {
 	json=" -json-gz $(pwd)/${NAME}.genes.json.gz "
 	name=" -dataset-name ${NAME} "
 
-	cmd="$nr $kegg $gff $faa $ffn $tax $bins $db $json $name"
+	titles_mount=""
+	titles=""
+	if [ ! -z "$TITLES" ]
+	then
+                titles=" -title-tsv $TITLES "
+		titles_mount=" -v $TITLES:$TITLES "
+	fi
+
+	cmd="$nr $kegg $gff $faa $ffn $tax $bins $db $json $name $titles "
 
 	if [ ! -z "$DEBUG_CHECK" ]
 	then
 		echo $cmd
 	fi
 
-	docker run -i $DBMOUNT -v $(pwd):$(pwd) -v $WORK_DIR:$WORK_DIR -v ${OUTPUT_PATH}:${OUTPUT_PATH} quay.io/emgb/annotatedgenes2json:2.3.1 $cmd
+	docker run -i $DBMOUNT -v $(pwd):$(pwd) ${titles_mount}  -v $WORK_DIR:$WORK_DIR -v ${OUTPUT_PATH}:${OUTPUT_PATH} quay.io/emgb/annotatedgenes2json:2.5.0 $cmd
 }
 
 
@@ -110,6 +120,9 @@ help()
 	echo "              -- (Examples: bacmet20_predicted, ncbi_nr)"
 	echo "  --db        -- emgb specific kegg database"
 	echo "  --name      -- sample name, e.g. the SAMPLE in the paths above"
+	echo "  --titles    -- Custom .tsv file mapping IDs to Subject Titles extracted from FASTA (optional)."
+	echo "              -- The following link explains how to create the corresponding tsv file."
+	echo "              -- https://gitlab.ub.uni-bielefeld.de/cmg/emgb/annotatedgenes2json#use-cases"
 	echo "  --type      -- if other then Illumina: ONT/Hybrid"
 	echo "  --workdir   -- absolute path to Nextflow work directory"
 	echo "  --help      -- help page"