Merge pull request #152 from ewels/version-1.5

Bump version to v1.5
nf-core · Apr 9, 2020 · d760335 · d760335
2 parents 50a5258 + 0ffdf85
commit d760335
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Showing 5 changed files with 12 additions and 13 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -16,11 +16,11 @@ jobs:
         aligner: ['bismark', 'bismark_hisat', 'bwameth']
         include:
           - aligner: 'bismark'
-            options: --bismark_index ${GITHUB_WORKSPACE}/results/reference_genome/BismarkIndex/
+            ref_index: --bismark_index results/reference_genome/BismarkIndex/
           - aligner: 'bismark_hisat'
-            options: --bismark_index ${GITHUB_WORKSPACE}/results/reference_genome/BismarkIndex/
+            ref_index: --bismark_index results/reference_genome/BismarkIndex/
           - aligner: 'bwameth'
-            options: --bwa_meth_index ${GITHUB_WORKSPACE}/results/reference_genome/genome.fa
+            ref_index: --bwa_meth_index results/reference_genome/genome.fa
     steps:
       - uses: actions/checkout@v2
       - name: Install Nextflow
@@ -30,10 +30,9 @@ jobs:
       - name: Pull docker image
         run: |
           docker pull nfcore/methylseq:dev
-          docker tag nfcore/methylseq:dev nfcore/methylseq:1.4.1
+          docker tag nfcore/methylseq:dev nfcore/methylseq:1.5
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --save_reference
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.options}}
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,6 @@
 # nf-core/methylseq
 
-## [v1.4.1](https://github.com/nf-core/methylseq/releases/tag/1.4.1) - 2020-04-08
+## [v1.5](https://github.com/nf-core/methylseq/releases/tag/1.5) - 2020-04-09
 
 ### New features
 
@@ -11,7 +11,7 @@
 
 ### Software updates
 
-* _new dependency_: pigz `2.3.4`
+* _New_: pigz `2.3.4`
 * Python base `2.7` > `3.7.3`
 * FastQC `0.11.8` > `0.11.9`
 * TrimGalore! `0.6.4` > `0.6.5`

diff --git a/Dockerfile b/Dockerfile
@@ -7,7 +7,7 @@ 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-methylseq-1.4.1/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-methylseq-1.5/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-methylseq-1.4.1 > nf-core-methylseq-1.4.1.yml
+RUN conda env export --name nf-core-methylseq-1.5 > nf-core-methylseq-1.5.yml
diff --git a/environment.yml b/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-methylseq-1.4.1
+name: nf-core-methylseq-1.5
 channels:
   - conda-forge
   - bioconda

diff --git a/nextflow.config b/nextflow.config
@@ -80,7 +80,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/methylseq:1.4.1'
+process.container = 'nfcore/methylseq:1.5'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -148,7 +148,7 @@ manifest {
   description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.4.1'
+  version = '1.5'
 }
 
 // Function to ensure that resource requirements don't go beyond