fix virsorter filtering when there are no class 1,2,3,4 detections

replikation · Feb 20, 2024 · b04bfa4 · b04bfa4
1 parent 3a049ea
commit b04bfa4
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Showing 3 changed files with 19 additions and 10 deletions.
diff --git 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
@@ -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
         """
 }
diff --git 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
         """
 }