condense and rename phylo-env to environment.yaml

.github/workflows/install.yaml

@@ -57,5 +57,6 @@ jobs:
           CONDA_ENV: "phylo-env"
         shell: bash -l {0}
         run: |
+          nextflow pull ktmeaton/plague-phylogeography
           nextflow pull ktmeaton/plague-phylogeography -r ${NF_REV}
-          conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/phylo-env.yaml
+          conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/environment.yaml

CHANGELOG.md

@@ -30,6 +30,7 @@ and this project "attempts" to adhere to [Semantic Versioning](http://semver.org
 ### Changed
 
 - Rename pipeline.nf to main.nf for nextflow pull compatibility
+- Condense phylo-env environment files and rename to environment.yaml
 - Start moving config files to config/ directory
 
 ## [v0.1.3] - 2020-05-28 - DHSI2020 Exhibit

README.md

@@ -35,17 +35,21 @@ wget -qO- get.nextflow.io | bash
 sudo mv nextflow /usr/local/bin/
 ```
 
-Pull the ktmeaton/plague-phylogeography pipeline and create a conda environment.
+Pull the ktmeaton/plague-phylogeography pipeline and create a conda environment.  
+(Expect this to take >10min)
 
 ```bash
 nextflow pull ktmeaton/plague-phylogeography
-conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/phylo-env.yaml
+conda env create -f  ~/.nextflow/assets/ktmeaton/plague-phylogeography/environment.yaml
 ```
 
 Pull the nf-core/eager pipeline and create a conda environment.
+Version control nf-core/eager to revision: 7b51863957.  
+(Expect this to take >10min)
 
 ```bash
-nextflow pull nf-core/eager -r dev
+nextflow pull nf-core/eager
+nextflow pull nf-core/eager -r 7b51863957
 conda env create -f ~/.nextflow/assets/nf-core/eager/environment.yml
 ```
 

nextflow.config

@@ -183,7 +183,7 @@ manifest {
 }
 
 // Process
-//process.conda = "$baseDir/phylo-env.yaml"
+//process.conda = "$baseDir/environment.yaml"
 
 
 // Function to ensure that resource requirements don't go beyond