bump version

.dockerignore

@@ -1,4 +1,14 @@
 .git
-pipeline-nanopore-ref-isoforms
+test_data
+bin
+CHANGELOG.md
+data
+lib
+LICENSE
+main.nf
+nextflow.config
 README.md
 test_data
+# we typically run tests with outputs to these:
+output
+work

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file.
 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).
 
+## [v0.2.1]
+### Changed
+- Update project with latest practices from wf-template.
+- Use `mamba` by default when using conda profile.
+### Fixed
+- Incorrect specification of conda environment file location.
+
 ## [v0.2.0]
 ### Changed
 - Rework workflow to use new medaka methodology for improved robustness of results.

nextflow.config

@@ -12,7 +12,7 @@ params {
     chunk_size = 1000000
     run_prokka = false
     prokka_opts = ""
-    wfversion = "v0.2.0"
+    wfversion = "v0.2.1"
     aws_image_prefix = null
     aws_queue = null
 }
@@ -54,17 +54,15 @@ profiles {
         }
         process {
             withLabel:containerCPU {
-                conda = "environment.yaml"
-            }
-            withLabel:containerGPU {
-                conda = "environment.yaml"
+                conda = "${projectDir}/environment.yaml"
             }
             withLabel:prokka {
-                conda = "environment_prokka.yaml"
+                conda = "${projectDir}/environment_prokka.yaml"
             }
         }
         conda {
              cacheDir = ""
+             useMamba = true
         }
     }