Merge pull request #177 from nf-core/patch

1.2.2 patch release to fix Conda environment and enable DSL1 in the nextflow.config

.github/workflows/ci.yml

@@ -35,13 +35,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/atacseq:1.2.1
+        run: docker build --no-cache . -t nfcore/atacseq:1.2.2
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/atacseq:dev
-          docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.1
+          docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.2
 
       - name: Install Nextflow
         run: |
@@ -75,13 +75,13 @@ jobs:
 
       - name: Build new docker image
         if: env.GIT_DIFF
-        run: docker build --no-cache . -t nfcore/atacseq:1.2.1
+        run: docker build --no-cache . -t nfcore/atacseq:1.2.2
 
       - name: Pull docker image
         if: ${{ !env.GIT_DIFF }}
         run: |
           docker pull nfcore/atacseq:dev
-          docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.1
+          docker tag nfcore/atacseq:dev nfcore/atacseq:1.2.2
 
       - name: Install Nextflow
         run: |

CHANGELOG.md

@@ -3,6 +3,14 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## [1.2.2] - 2022-04-29
+
+* Minor patch release to fix Conda environment and enable DSL1 by default in the `nextflow.config`.
+### `Dependencies`
+
+* Update r-base `3.6.2` -> `3.6.3`
+* Update r-xfun `0.15`  -> `0.22`
+
 ## [1.2.1] - 2020-07-29
 
 * [#118](https://github.com/nf-core/atacseq/issues/118) - Minor patch release to update pipeline schema

Dockerfile

@@ -7,10 +7,10 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-atacseq-1.2.1/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-atacseq-1.2.2/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-atacseq-1.2.1 > nf-core-atacseq-1.2.1.yml
+RUN conda env export --name nf-core-atacseq-1.2.2 > nf-core-atacseq-1.2.2.yml
 
 # Instruct R processes to use these empty files instead of clashing with a local version
 RUN touch .Rprofile

environment.yml

@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: nf-core-atacseq-1.2.1
+name: nf-core-atacseq-1.2.2
 channels:
   - conda-forge
   - bioconda
@@ -11,7 +11,7 @@ dependencies:
   - conda-forge::markdown=3.2.2
   - conda-forge::pymdown-extensions=7.1
   - conda-forge::pygments=2.6.1
-  - conda-forge::r-base=3.6.2
+  - conda-forge::r-base=3.6.3
   - conda-forge::r-optparse=1.6.6
   - conda-forge::r-rcolorbrewer=1.1_2
   - conda-forge::r-reshape2=1.4.4
@@ -21,7 +21,7 @@ dependencies:
   - conda-forge::r-pheatmap=1.0.12
   - conda-forge::r-lattice=0.20_41
   - conda-forge::r-upsetr=1.4.0
-  - conda-forge::r-xfun=0.15
+  - conda-forge::r-xfun=0.22
   - conda-forge::gawk=5.1.0
   - conda-forge::pigz=2.3.4               ## Required for TrimGalore multi-threading
 

nextflow.config

@@ -5,6 +5,10 @@
  * Default config options for all environments.
  */
 
+// From nextflow version 22.04.0, DSL1 becomes the default mode
+// see here: https://www.nextflow.io/blog/2022/evolution-of-nextflow-runtime.html
+nextflow.enable.dsl = 1
+
 // Global default params, used in configs
 params {
 
@@ -99,7 +103,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/atacseq:1.2.1'
+process.container = 'nfcore/atacseq:1.2.2'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'