The $somatic_functional_indel_vcf has a header that was counted, resu…

…lting in a wrong branch choice for PDF creation. Furthermore, a branch for no functional variants was added.

resources/analysisTools/indelCallingWorkflow/filter_vcf.sh

@@ -71,10 +71,14 @@ ${PERL_BINARY} ${TOOL_PLATYPUS_INDEL_EXTRACTOR} --bgzip=${BGZIP_BINARY} --tabix=
 
 [[ ! -d ${screenshot_dir} ]] && mkdir ${screenshot_dir} && cd ${screenshot_dir}
 
-functional_var_count=`cat ${somatic_functional_indel_vcf} | wc -l | cut -f1 -d " "`
+functional_var_count=`cat ${somatic_functional_indel_vcf} | tail -n +2 | wc -l | cut -f1 -d " "`
 
-if [[ $functional_var_count -le $MAX_VARIANT_SCREENSHOTS ]]
-then
+if [[ $functional_var_count -eq 0 ]]; then
+    printf "WARNING: No functional variants present in ${somatic_functional_indel_vcf}\n"
+    $RSCRIPT_BINARY "$TOOL_TEXT_PDF" "WARNING: No functional variants." \
+        > "$combined_screen_shots"
+
+elif [[ $functional_var_count -le $MAX_VARIANT_SCREENSHOTS ]]; then
 
     if [[ "${isControlWorkflow}" == true ]]; then
         ${PYTHON_BINARY} ${TOOL_SCREENSHOT} \
@@ -105,8 +109,8 @@ then
 
     ${GHOSTSCRIPT_BINARY} -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=${combined_screen_shots} ${sorted}
 else
-    printf "WARNINGS: No screenshots done, more than $MAX_VARIANT_SCREENSHOTS (cvalue - MAX_VARIANT_SCREENSHOTS) functional variants present in ${somatic_functional_indel_vcf}\n"
-    $RSCRIPT_BINARY "$TOOL_TEXT_PDF" "WARNING\nNo screenshots done. More than $MAX_VARIANT_SCREENSHOTS functional variants." \
+    printf "WARNING: No screenshots done, more than $MAX_VARIANT_SCREENSHOTS (cvalue - MAX_VARIANT_SCREENSHOTS) functional variants present in ${somatic_functional_indel_vcf}\n"
+    $RSCRIPT_BINARY "$TOOL_TEXT_PDF" "WARNING: No screenshots done. More than $MAX_VARIANT_SCREENSHOTS functional variants." \
         > "$combined_screen_shots"
 fi