From 62528919b0b5c618cb16d134d0818d116acb2869 Mon Sep 17 00:00:00 2001
From: Lauren Coombe <lauren.e.coombe@gmail.com>
Date: Mon, 5 Feb 2024 11:50:26 -0800
Subject: [PATCH] Prepare for release v1.1.4 (#105)

---
 README.md         | 4 ++--
 bin/ntjoin_run.py | 2 +-
 ntJoin            | 6 +++---
 setup.py          | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/README.md b/README.md
index 16a7697..0b63c84 100644
--- a/README.md
+++ b/README.md
@@ -125,7 +125,7 @@ ntJoin assemble target=my_scaffolds.fa target_weight=1 reference_config=config_f
 
 #### Installing ntJoin using Conda
 ```sh
-conda install -c bioconda -c conda-forge ntjoin=1.1.3
+conda install -c bioconda -c conda-forge ntjoin=1.1.4
 ```
 
 #### Installing ntJoin using Brew
@@ -136,7 +136,7 @@ brew install brewsci/bio/ntjoin
 
 #### Installing ntJoin from the source code
 ```sh
-curl -L --output ntJoin-1.1.3.tar.gz https://github.com/bcgsc/ntJoin/releases/download/v1.1.3/ntJoin-1.1.3.tar.gz && tar xvzf ntJoin-1.1.3.tar.gz 
+curl -L --output ntJoin-1.1.4.tar.gz https://github.com/bcgsc/ntJoin/releases/download/v1.1.4/ntJoin-1.1.4.tar.gz && tar xvzf ntJoin-1.1.4.tar.gz 
 ```
 
 ## Dependencies
diff --git a/bin/ntjoin_run.py b/bin/ntjoin_run.py
index 271c5f8..435870a 100755
--- a/bin/ntjoin_run.py
+++ b/bin/ntjoin_run.py
@@ -35,7 +35,7 @@ def parse_arguments():
                                     "increasing/decreasing to assign contig orientation [90]\n "
                                     "Note: Only used with --mkt is NOT specified", default=90, type=int)
     parser.add_argument('-t', help="Number of threads for multiprocessing [1]", default=1, type=int)
-    parser.add_argument("-v", "--version", action='version', version='ntJoin v1.1.3')
+    parser.add_argument("-v", "--version", action='version', version='ntJoin v1.1.4')
     parser.add_argument("--agp", help="Output AGP file describing scaffolds", action="store_true")
     parser.add_argument("--no_cut", help="Do not cut input contigs, place in most representative path",
                         action="store_true")
diff --git a/ntJoin b/ntJoin
index 428d7bb..67559ee 100755
--- a/ntJoin
+++ b/ntJoin
@@ -2,7 +2,7 @@
 
 # ntJoin: Scaffold assemblies using reference assemblies and minimizer graphs
 # Written by Lauren Coombe @lcoombe
-# ntJoin v1.1.3
+# ntJoin v1.1.4
 
 # Input files
 target=None
@@ -117,7 +117,7 @@ endif
 help:
 	@echo ""
 	@echo "ntJoin: Scaffolding assemblies using reference assemblies and minimizer graphs"
-	@echo "ntJoin v1.1.3"
+	@echo "ntJoin v1.1.4"
 	@echo "Usage: ntJoin assemble target=<target scaffolds> references='List of reference assemblies' reference_weights='List of weights per reference assembly'"
 	@echo ""
 	@echo "Options:"
@@ -186,7 +186,7 @@ ifeq ($(ref), None)
 endif
 
 version:
-	@echo "ntJoin v1.1.3"
+	@echo "ntJoin v1.1.4"
 	@echo "Written by Lauren Coombe (lcoombe@bcgsc.ca)"
 
 check_install:
diff --git a/setup.py b/setup.py
index 45eb951..9f53fe8 100644
--- a/setup.py
+++ b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="ntJoin",
-    version="1.1.3",
+    version="1.1.4",
     author="Lauren Coombe",
     author_email="lcoombe@bcgsc.ca",
     description="Genome assembly scaffolder using minimizer graphs",