manual bump-version 2.6

nf-core · May 19, 2020 · d21320d · d21320d
1 parent 212e096
commit d21320d
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Showing 10 changed files with 27 additions and 27 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,7 +6,7 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
     steps:
       - checkout
       - setup_remote_docker
@@ -20,28 +20,28 @@ jobs:
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   vepgrch37: &buildvep
     docker:
@@ -50,7 +50,7 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
     steps:
       - checkout
       - setup_remote_docker
@@ -66,31 +66,31 @@ jobs:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.6
 
 workflows:
   version: 2

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -45,8 +45,8 @@ jobs:
           NXF_VER: '19.10.0'
       - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev
-          docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
+          docker pull nfcore/sarek:2.6
+          docker pull nfcore/sarek${{ matrix.tools }}:2.6.${{ matrix.species }}
       - name: Run annotation test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
 
@@ -67,7 +67,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.6
       - name: Get test data
         run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
       - name: Run germline test
@@ -95,7 +95,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.6
       - name: Run test for minimal genomes
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skipQC all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
@@ -116,7 +116,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.6
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
 
@@ -147,6 +147,6 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '19.10.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.6
       - name: Run ${{ matrix.tool }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 
 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).
 
-## [2.6dev] - Piellorieppe
+## [2.6] - Piellorieppe
 
 Piellorieppe is one of the main massif in the Sarek National Park.
 

diff --git a/conf/base.config b/conf/base.config
@@ -68,11 +68,11 @@ process {
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withName:Snpeff {
-    container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"}
+    container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.6' : "nfcore/sareksnpeff:2.6.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withLabel:VEP {
-    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:dev' : "nfcore/sarekvep:dev.${params.genome}"}
+    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:2.6' : "nfcore/sarekvep:2.6.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
 }
diff --git a/conf/test.config b/conf/test.config
@@ -27,11 +27,11 @@ params {
 
 process {
   withName:Snpeff {
-    container = 'nfcore/sareksnpeff:dev.GRCh37'
+    container = 'nfcore/sareksnpeff:2.6.WBcel235'
     maxForks = 1
   }
   withLabel:VEP {
-    container = 'nfcore/sarekvep:dev.GRCh37'
+    container = 'nfcore/sarekvep:2.6.WBcel235'
     maxForks = 1
   }
 }
diff --git a/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile
@@ -9,7 +9,7 @@ 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-sarek-snpeff-2.6dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-snpeff-2.6/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
@@ -19,4 +19,4 @@ ARG SNPEFF_CACHE_VERSION=86
 RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-sarek-snpeff-2.6dev > nf-core-sarek-snpeff-2.6dev.yml
+RUN conda env export --name nf-core-sarek-snpeff-2.6 > nf-core-sarek-snpeff-2.6.yml
diff --git a/containers/snpeff/environment.yml b/containers/snpeff/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-sarek-snpeff-2.6dev
+name: nf-core-sarek-snpeff-2.6
 channels:
   - conda-forge
   - bioconda

diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile
@@ -9,7 +9,7 @@ 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-sarek-vep-2.6dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-vep-2.6/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
@@ -27,4 +27,4 @@ RUN vep_install \
   --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-sarek-vep-2.6dev > nf-core-sarek-vep-2.6dev.yml
+RUN conda env export --name nf-core-sarek-vep-2.6 > nf-core-sarek-vep-2.6.yml
diff --git a/containers/vep/environment.yml b/containers/vep/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-sarek-vep-2.6dev
+name: nf-core-sarek-vep-2.6
 channels:
   - conda-forge
   - bioconda

diff --git a/docs/images/sarek_workflow.png b/docs/images/sarek_workflow.png