From 3e281b756eb49df87271b4b276c1f66343b666a6 Mon Sep 17 00:00:00 2001
From: pdiakumis <peterdiakumis@gmail.com>
Date: Fri, 8 Nov 2024 12:46:34 +1100
Subject: [PATCH] =?UTF-8?q?Bump=20version:=201.1.4=20=E2=86=92=201.1.5?=
MIME-Version: 1.0
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---
 .bumpversion.toml                          | 2 +-
 .github/workflows/conda_docker_pkgdown.yml | 2 +-
 DESCRIPTION                                | 2 +-
 README.md                                  | 8 ++++----
 deploy/conda/env/yaml/rnasum.yaml          | 2 +-
 deploy/conda/recipe/meta.yaml              | 2 +-
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.bumpversion.toml b/.bumpversion.toml
index f8f52af0..90ed56a0 100644
--- a/.bumpversion.toml
+++ b/.bumpversion.toml
@@ -1,5 +1,5 @@
 [tool.bumpversion]
-current_version = "1.1.4"
+current_version = "1.1.5"
 search = "{current_version}"
 replace = "{new_version}"
 message = "Bump version: {current_version} → {new_version}"
diff --git a/.github/workflows/conda_docker_pkgdown.yml b/.github/workflows/conda_docker_pkgdown.yml
index d0ec4769..33cfadb8 100644
--- a/.github/workflows/conda_docker_pkgdown.yml
+++ b/.github/workflows/conda_docker_pkgdown.yml
@@ -9,7 +9,7 @@ env:
   recipe_path: deploy/conda/recipe
   env_yaml_path: deploy/conda/env/yaml
   env_lock_path: deploy/conda/env/lock
-  VERSION: '1.1.4' # bump
+  VERSION: '1.1.5' # bump
 
 jobs:
   condarise-dockerise-document:
diff --git a/DESCRIPTION b/DESCRIPTION
index ec49333f..d5ad6f8b 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: RNAsum
 Title: A Robust Tool for Performing Transcriptome Profiling on Cancer Data
-Version: 1.1.4
+Version: 1.1.5
 Authors@R: 
     c(person(given = "Sehrish",
              family = "Kanwal",
diff --git a/README.md b/README.md
index eacc1cda..5a8cee33 100755
--- a/README.md
+++ b/README.md
@@ -197,7 +197,7 @@ export PATH="${rnasum_cli}:${PATH}"
 ```
 
     $ rnasum.R --version
-    1.1.4 
+    1.1.5 
 
     $ rnasum.R --help
     Usage
@@ -253,9 +253,6 @@ export PATH="${rnasum_cli}:${PATH}"
     --log
             Log2 transform data before normalisation.
 
-    --sv_tsv=SV_TSV
-            File path to text file with genes related to structural variation.
-
     --norm=NORM
             Normalisation method.
 
@@ -295,6 +292,9 @@ export PATH="${rnasum_cli}:${PATH}"
     --subject_id=SUBJECT_ID
             Subject ID.
 
+    --sv_tsv=SV_TSV
+            File path to text file with genes related to structural variation.
+
     --top_genes=TOP_GENES
             Number of top ranked genes to be presented in report.
 
diff --git a/deploy/conda/env/yaml/rnasum.yaml b/deploy/conda/env/yaml/rnasum.yaml
index 23cc968a..60d3e7aa 100644
--- a/deploy/conda/env/yaml/rnasum.yaml
+++ b/deploy/conda/env/yaml/rnasum.yaml
@@ -6,4 +6,4 @@ channels:
   - bioconda
 
 dependencies:
-  - r-rnasum ==1.1.4 # bump
+  - r-rnasum ==1.1.5 # bump
diff --git a/deploy/conda/recipe/meta.yaml b/deploy/conda/recipe/meta.yaml
index f6a766cc..33f27cbf 100644
--- a/deploy/conda/recipe/meta.yaml
+++ b/deploy/conda/recipe/meta.yaml
@@ -1,6 +1,6 @@
 package:
   name: r-rnasum
-  version: 1.1.4 # bump
+  version: 1.1.5 # bump
 
 source:
   path: ../../../