From b04bfa4eca9fabfc3f85ee362f62e3ad7c432449 Mon Sep 17 00:00:00 2001
From: hoelzer <hoelzer.martin@gmail.com>
Date: Tue, 20 Feb 2024 10:15:05 +0100
Subject: [PATCH] fix virsorter filtering when there are no class 1,2,3,4
 detections

---
 workflows/process/sourmash/sourmash.nf             |  1 +
 workflows/process/virsorter/filter_virsorter.nf    | 14 +++++++++-----
 .../virsorter_virome/filter_virsorter_virome.nf    | 14 +++++++++-----
 3 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/workflows/process/sourmash/sourmash.nf b/workflows/process/sourmash/sourmash.nf
index 0266624..005df01 100644
--- a/workflows/process/sourmash/sourmash.nf
+++ b/workflows/process/sourmash/sourmash.nf
@@ -23,6 +23,7 @@ process sourmash {
           filename=\$(basename \${tempfile} .fa.sig.temporary)
           prediction_value=\$(grep -v "similarity,md5,filename,name,query_filename,query_name,query_md5,ani" \${tempfile} |sort -r -k1 | awk 'NR == 1' | cut -d "," -f1 )
       
+	  touch ${name}_\${PWD##*/}.list
           if [ \$value -gt 0 ] 
             then echo "\$filename,\$prediction_value" >> ${name}_\${PWD##*/}.list
           fi
diff --git a/workflows/process/virsorter/filter_virsorter.nf b/workflows/process/virsorter/filter_virsorter.nf
index 06bda84..a014c6f 100644
--- a/workflows/process/virsorter/filter_virsorter.nf
+++ b/workflows/process/virsorter/filter_virsorter.nf
@@ -26,10 +26,14 @@ process filter_virsorter {
                 echo "\$line,0" >> pro_phage_virsorter.tsv
             fi
         done < virsorter_categorized_contigs_*.list
-        grep ">" virsorter_phage.tsv | \\
-        sed -e s/\\>VIRSorter_//g | \\
-        sed -e s/\\-cat_[1-3]//g | \\
-        awk -F, '{print \$1, \$2}' OFS="\\t"  > virsorter_\${PWD##*/}.tsv
-        rm virsorter_phage.tsv
+	if [ -s virsorter_phage.tsv ]; then
+           grep ">" virsorter_phage.tsv | \\
+           sed -e s/\\>VIRSorter_//g | \\
+           sed -e s/\\-cat_[1-3]//g | \\
+           awk -F, '{print \$1, \$2}' OFS="\\t"  > virsorter_\${PWD##*/}.tsv
+           rm virsorter_phage.tsv
+	else
+	 touch virsorter_\${PWD##*/}.tsv
+	fi
         """
 }
\ No newline at end of file
diff --git a/workflows/process/virsorter_virome/filter_virsorter_virome.nf b/workflows/process/virsorter_virome/filter_virsorter_virome.nf
index 98380a8..03e7d16 100644
--- a/workflows/process/virsorter_virome/filter_virsorter_virome.nf
+++ b/workflows/process/virsorter_virome/filter_virsorter_virome.nf
@@ -27,10 +27,14 @@ process filter_virsorter_virome {
             fi
         done < virsorter_categorized_contigs_*.list
 
-        grep ">" virsorter_phage.tsv | \\
-        sed -e s/\\>VIRSorter_//g | \\
-        sed -e s/\\-cat_[1-3]//g | \\
-        awk -F, '{print \$1, \$2}' OFS="\\t" > virsorter-virome_\${PWD##*/}.tsv
-        rm virsorter_phage.tsv
+	if [ -s virsorter_phage.tsv ]; then
+           grep ">" virsorter_phage.tsv | \\
+           sed -e s/\\>VIRSorter_//g | \\
+           sed -e s/\\-cat_[1-3]//g | \\
+           awk -F, '{print \$1, \$2}' OFS="\\t" > virsorter-virome_\${PWD##*/}.tsv
+           rm virsorter_phage.tsv
+	else
+	   touch virsorter-virome_\${PWD##*/}.tsv
+	fi
         """
 }