From 4572252e6114937ce05ffd2e8fae60602cc0582a Mon Sep 17 00:00:00 2001
From: Florian Zwagemaker <f.zwagemaker@gmail.com>
Date: Wed, 3 Jul 2024 15:09:51 +0200
Subject: [PATCH 1/2] deps: Update conda environment files to remove the
 'intel' channel

docs: update documentation page accordingly
---
 .gitignore                            |  4 +++-
 SARS2seq/workflow/envs/Alignment.yaml |  1 -
 SARS2seq/workflow/envs/Clean.yaml     |  1 -
 SARS2seq/workflow/envs/Consensus.yaml |  1 -
 SARS2seq/workflow/envs/Mutations.yaml |  1 -
 SARS2seq/workflow/envs/Typing.yaml    |  1 -
 docs/index.md                         |  5 +----
 env.yml                               |  1 -
 mamba-env.yaml                        | 16 ----------------
 9 files changed, 4 insertions(+), 27 deletions(-)
 delete mode 100644 mamba-env.yaml

diff --git a/.gitignore b/.gitignore
index bccd48d..120aeb0 100644
--- a/.gitignore
+++ b/.gitignore
@@ -130,4 +130,6 @@ dmypy.json
 .pyre/
 
 # IDE
-.vscode/
\ No newline at end of file
+.vscode/
+
+test*
\ No newline at end of file
diff --git a/SARS2seq/workflow/envs/Alignment.yaml b/SARS2seq/workflow/envs/Alignment.yaml
index 42d1cda..fbeedbe 100644
--- a/SARS2seq/workflow/envs/Alignment.yaml
+++ b/SARS2seq/workflow/envs/Alignment.yaml
@@ -2,7 +2,6 @@ name: Reference_alignment
 channels:
   - bioconda
   - conda-forge
-  - intel
   - nodefaults
 dependencies:
   - python=3.7
diff --git a/SARS2seq/workflow/envs/Clean.yaml b/SARS2seq/workflow/envs/Clean.yaml
index 2a4ef0b..be139c3 100644
--- a/SARS2seq/workflow/envs/Clean.yaml
+++ b/SARS2seq/workflow/envs/Clean.yaml
@@ -2,7 +2,6 @@ name: QC_and_cleanup
 channels:
   - bioconda
   - conda-forge
-  - intel
   - nodefaults
 dependencies:
   - python=3.8
diff --git a/SARS2seq/workflow/envs/Consensus.yaml b/SARS2seq/workflow/envs/Consensus.yaml
index 4e18609..c5b6db2 100644
--- a/SARS2seq/workflow/envs/Consensus.yaml
+++ b/SARS2seq/workflow/envs/Consensus.yaml
@@ -2,7 +2,6 @@ name: Consensus
 channels:
   - bioconda
   - conda-forge
-  - intel
   - nodefaults
 dependencies:
   - python=3.7
diff --git a/SARS2seq/workflow/envs/Mutations.yaml b/SARS2seq/workflow/envs/Mutations.yaml
index c1917de..00f3171 100644
--- a/SARS2seq/workflow/envs/Mutations.yaml
+++ b/SARS2seq/workflow/envs/Mutations.yaml
@@ -2,7 +2,6 @@ name: Mutations
 channels:
   - bioconda
   - conda-forge
-  - intel
   - nodefaults
 dependencies:
   - bcftools==1.14
\ No newline at end of file
diff --git a/SARS2seq/workflow/envs/Typing.yaml b/SARS2seq/workflow/envs/Typing.yaml
index 2c84a69..85785eb 100644
--- a/SARS2seq/workflow/envs/Typing.yaml
+++ b/SARS2seq/workflow/envs/Typing.yaml
@@ -2,7 +2,6 @@ name: Typing
 channels:
   - bioconda
   - conda-forge
-  - intel
   - nodefaults
 dependencies:
   - python=3.7
diff --git a/docs/index.md b/docs/index.md
index 5199f9a..2abac62 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -36,10 +36,7 @@ git clone https://github.com/RIVM-bioinformatics/SARS2seq.git; cd SARS2seq; git
 1. Create the required conda-environment and install the necessary dependencies.  
     Copy and paste the code-snippet below in order to create the new conda-environment and directly activate it.  
     
-    `conda create --name SARS2seq -c conda-forge mamba python=3.7 -y; conda activate SARS2seq; mamba env update -f mamba-env.yaml`
-
-    You can also use the following snippet if the code-snippet above didn't work for you:  
-    `conda env create -f env.yml && conda activate SARS2seq`  
+    `mamba env create -f env.yml && conda activate SARS2seq`
     
     **The "SARS2seq" environment should now be active**  
 
diff --git a/env.yml b/env.yml
index b770c5c..78c0ad6 100644
--- a/env.yml
+++ b/env.yml
@@ -2,7 +2,6 @@ name: SARS2seq
 channels:
   - bioconda
   - conda-forge
-  - intel
   - nodefaults
 dependencies:
   - python=3.8
diff --git a/mamba-env.yaml b/mamba-env.yaml
deleted file mode 100644
index eaedca1..0000000
--- a/mamba-env.yaml
+++ /dev/null
@@ -1,16 +0,0 @@
-channels:
-  - bioconda
-  - conda-forge
-  - intel
-dependencies:
-  - python=3.7
-  - conda=4.11
-  - mamba
-  - drmaa==0.7.9
-  - snakemake==7.12.1
-  - tabulate==0.8.10
-  - biopython==1.79
-  - pyyaml==6.0
-  - urllib3>=1.26
-  - fpdf==1.7.2
-  - pip

From b757c552bbfea80b62dd0e07aa330543cf3423e9 Mon Sep 17 00:00:00 2001
From: ids-bioinformatics
 <81251468+ids-bioinformatics@users.noreply.github.com>
Date: Wed, 3 Jul 2024 15:10:15 +0200
Subject: [PATCH 2/2] chore(main): release 0.6.8

---
 CHANGELOG.md        | 12 ++++++++++++
 SARS2seq/version.py |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8976a88..2ad204a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,17 @@
 # Changelog
 
+## [0.6.8](https://github.com/RIVM-bioinformatics/SARS2seq/compare/v0.6.7...v0.6.8) (2024-07-03)
+
+
+### Dependencies
+
+* Update conda environment files to remove the 'intel' channel ([4572252](https://github.com/RIVM-bioinformatics/SARS2seq/commit/4572252e6114937ce05ffd2e8fae60602cc0582a))
+
+
+### Documentation
+
+* update documentation page accordingly ([4572252](https://github.com/RIVM-bioinformatics/SARS2seq/commit/4572252e6114937ce05ffd2e8fae60602cc0582a))
+
 ## [0.6.7](https://github.com/RIVM-bioinformatics/SARS2seq/compare/v0.6.6...v0.6.7) (2024-04-04)
 
 
diff --git a/SARS2seq/version.py b/SARS2seq/version.py
index f6104e0..afd45a4 100644
--- a/SARS2seq/version.py
+++ b/SARS2seq/version.py
@@ -1 +1 @@
-__version__ = "0.6.7"
+__version__ = "0.6.8"