deps: explicitly state the nodefaults channel in all environments

deps: solve minor installation hassles for the main environment

SARS2seq/workflow/envs/Alignment.yaml

@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.7
   - minimap2==2.24

SARS2seq/workflow/envs/Clean.yaml

@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.8
   - ampligone==1.2.1

SARS2seq/workflow/envs/Consensus.yaml

@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.7
   - libffi==3.3
@@ -14,5 +15,6 @@ dependencies:
   - tqdm=4.62
   - pip
   - pip:
-    - gffpandas>=1.2
-    - git+https://github.com/RIVM-bioinformatics/TrueConsense.git@v0.5.0
+      #this is temporary until gffpandas has a patched version released on conda/pypi or when we port the required function in TrueConsense to AminoExtract
+    - git+https://github.com/florianzwagemaker/gffpandas.git@main
+    - git+https://github.com/RIVM-bioinformatics/TrueConsense.git@v0.5.1

SARS2seq/workflow/envs/Mutations.yaml

@@ -3,5 +3,6 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - bcftools==1.14

SARS2seq/workflow/envs/Typing.yaml

@@ -3,6 +3,7 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
   - python=3.7
   - libffi==3.3

env.yml

@@ -3,10 +3,11 @@ channels:
   - bioconda
   - conda-forge
   - intel
+  - nodefaults
 dependencies:
-  - python=3.7
-  - conda=4.11
-  - mamba
+  - python=3.8
+  # - conda=4.11
+  - mamba>1.0
   - drmaa==0.7.9
   - snakemake==7.12.1
   - tabulate==0.8.10