From 6db74cd48c22304d01b1c665ba698de4c568dd1e Mon Sep 17 00:00:00 2001
From: "Michael G. Campana" <campanam@si.edu>
Date: Thu, 19 Jan 2023 11:39:35 -0500
Subject: [PATCH 1/3] summarizeDNM glitch fix

Potential fix to summarizeDNM when no candidates found
---
 CHANGELOG.Md  |  3 +++
 ratestools.nf | 11 ++++++++---
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.Md b/CHANGELOG.Md
index ca42e1f..0f1e7b2 100644
--- a/CHANGELOG.Md
+++ b/CHANGELOG.Md
@@ -315,6 +315,9 @@ First version integrated into pipeline
 Initial script (plotDPGQ-clean.R)  
 
 ## ratestools  
+### Version 0.5.11  
+Fixed glitch in summarizeDNM when no candidate sites found  
+
 ### Version 0.5.10  
 Update file headers  
 Contig length filtration  
diff --git a/ratestools.nf b/ratestools.nf
index 60884f8..7f7ad0b 100755
--- a/ratestools.nf
+++ b/ratestools.nf
@@ -1,6 +1,6 @@
 #!/usr/bin/env nextflow
 
-/* RatesTools version 0.5.10
+/* RatesTools version 0.5.11
 Michael G. Campana and Ellie E. Armstrong, 2020-2023
 Smithsonian Institution and Stanford University
 
@@ -932,8 +932,13 @@ process summarizeDNM {
 		val=`grep -n \'#CHROM\' \$sumlog | cut -d \':\' -f 1`
 		total=`wc -l \$sumlog | cut -d \' \' -f 1`
 		let lncount=\$total-\$val
-		tail -n \$lncount \$sumlog > tmp.txt
-		cat header.txt tmp.txt | gzip > \${sumlog/_summary.log/_candidates.vcf.gz}
+		if [ $lncount -gt 0 ]; then
+			tail -n \$lncount \$sumlog > tmp.txt
+			cat header.txt tmp.txt | gzip > \${sumlog/_summary.log/_candidates.vcf.gz}
+		else
+			mv header.txt \${sumlog/_summary.log/_candidates.vcf}
+			gzip \${sumlog/_summary.log/_candidates.vcf}
+		fi
 	done
 	"""
 

From d499b502f4e7465551700f723fc30ccccf21eb80 Mon Sep 17 00:00:00 2001
From: "Michael G. Campana" <campanam@si.edu>
Date: Thu, 19 Jan 2023 11:48:43 -0500
Subject: [PATCH 2/3] escaping

---
 ratestools.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ratestools.nf b/ratestools.nf
index 7f7ad0b..b9ad078 100755
--- a/ratestools.nf
+++ b/ratestools.nf
@@ -932,7 +932,7 @@ process summarizeDNM {
 		val=`grep -n \'#CHROM\' \$sumlog | cut -d \':\' -f 1`
 		total=`wc -l \$sumlog | cut -d \' \' -f 1`
 		let lncount=\$total-\$val
-		if [ $lncount -gt 0 ]; then
+		if [ \$lncount -gt 0 ]; then
 			tail -n \$lncount \$sumlog > tmp.txt
 			cat header.txt tmp.txt | gzip > \${sumlog/_summary.log/_candidates.vcf.gz}
 		else

From 0558933aa417528cf011d91e8d45a6f35b4dc72d Mon Sep 17 00:00:00 2001
From: "Michael G. Campana" <campanam@si.edu>
Date: Thu, 19 Jan 2023 11:58:47 -0500
Subject: [PATCH 3/3] explicit bash

---
 ratestools.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ratestools.nf b/ratestools.nf
index b9ad078..6fab23b 100755
--- a/ratestools.nf
+++ b/ratestools.nf
@@ -916,6 +916,7 @@ process summarizeDNM {
 	path "${params.prefix}*_candidates.vcf.gz" into candidates_vcf_ch
 	
 	"""
+	#!/usr/bin/env bash
 	for file in ${params.prefix}*.log; do 
 		if [ ! -d \${file%_chr*.log} ]; then
 			mkdir \${file%_chr*.log}