From 2b0cb855b288680d58d31b346b1a84e76eee4e4d Mon Sep 17 00:00:00 2001
From: Guoying Qi <gq2@sanger.ac.uk>
Date: Thu, 14 Mar 2024 14:58:06 +0000
Subject: [PATCH 1/3] wrong fai channel name

---
 workflows/variantcalling.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/variantcalling.nf b/workflows/variantcalling.nf
index 642282e..45a9f83 100644
--- a/workflows/variantcalling.nf
+++ b/workflows/variantcalling.nf
@@ -104,7 +104,7 @@ workflow VARIANTCALLING {
        }
 
     }else{
-       ch_index
+       ch_fai
         .map { fai -> [ [ 'id': fai.baseName ], fai ] }
         .first()
         .set { ch_genome_index }

From acc0df03de4ca4dfcec052be62fd235f21283eb4 Mon Sep 17 00:00:00 2001
From: Guoying Qi <gq2@sanger.ac.uk>
Date: Thu, 14 Mar 2024 15:09:38 +0000
Subject: [PATCH 2/3] Preprare for the bug fix release

---
 CHANGELOG.md    | 27 ++++++++++++++++++++++++++-
 nextflow.config |  2 +-
 2 files changed, 27 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 03559d5..f244d2b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,32 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.1.1](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.1)] - Shang Zhou - [2024-02-02]
+## [[1.1.2](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.2)] - Shang Tang (patch 2) - [2024-03-14]
+
+### Enhancements & fixes
+
+- Bug fix when index fai file given for reference fasta file
+
+### Parameters
+
+This release with the following initial parameters:
+
+| Old parameter | New parameter |
+| ------------- | ------------- |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
+
+
+## [[1.1.1](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.1)] - Shang Tang (patch 1) - [2024-02-02]
 
 ### Enhancements & fixes
 
diff --git a/nextflow.config b/nextflow.config
index 934e6e7..ca837be 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -215,7 +215,7 @@ manifest {
     description     = """Variant calling pipeline for PacBio data using DeepVariant"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version = '1.1.1'
+    version = '1.1.2'
     doi             = 'https://doi.org/10.5281/zenodo.7890527'
 }
 

From 36132048965e22c975e1d1d168ddaeebb3730c18 Mon Sep 17 00:00:00 2001
From: sanger-tolsoft <105875386+sanger-tolsoft@users.noreply.github.com>
Date: Thu, 14 Mar 2024 15:22:14 +0000
Subject: [PATCH 3/3] [automated] Fix linting with Prettier

---
 CHANGELOG.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f244d2b..d111be4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,7 +27,6 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 
 > **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
 
-
 ## [[1.1.1](https://github.com/sanger-tol/variantcalling/releases/tag/1.1.1)] - Shang Tang (patch 1) - [2024-02-02]
 
 ### Enhancements & fixes