Restarting dev branch

.circleci/config.yml

@@ -10,11 +10,11 @@ jobs:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sareksnpeff:2.5.2.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+          command: docker build -t nfcore/sareksnpeff:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
       - run:
           command: |
             echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin
-            docker push nfcore/sareksnpeff:2.5.2.${GENOME}
+            docker push nfcore/sareksnpeff:dev.${GENOME}
 
   snpeffgrch38:
     << : *buildsnpeff
@@ -45,10 +45,10 @@ jobs:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sarekvep:2.5.2.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          command: docker build -t nfcore/sarekvep:dev.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
           no_output_timeout: 3h
       - run:
-          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:2.5.2.${GENOME}
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:dev.${GENOME}
 
   vepgrch38:
     << : *buildvep

.github/workflows/ci.yml

@@ -18,7 +18,7 @@ jobs:
       - name: Download and tag image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
@@ -39,9 +39,9 @@ jobs:
       - name: Download and tag images
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
           docker pull nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
-          docker tag nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }} nfcore/sarek${{ matrix.annotator }}:2.5.2.${{ matrix.specie }}
+          docker tag nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }} nfcore/sarek${{ matrix.annotator }}:dev.${{ matrix.specie }}
       - name: Run annotation test
         run: |
           nextflow run . -profile test_annotation,docker --verbose --tools ${{ matrix.annotator }}
@@ -58,7 +58,7 @@ jobs:
       - name: Download and tag image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Get test data
         run: |
           git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
@@ -84,7 +84,7 @@ jobs:
       - name: Download and tag image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run test for minimal genomes
         run: |
           nextflow run . -profile test,docker --skipQC all --verbose --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka
@@ -104,7 +104,7 @@ jobs:
       - name: Download and tag image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run targeted and splitfastq tests
         run: |
           nextflow run . -profile ${{ matrix.profile }},docker --verbose
@@ -124,7 +124,7 @@ jobs:
       - name: Download and tag image
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+          docker tag nfcore/sarek:dev nfcore/sarek:dev
       - name: Run variant calling test on specific tools
         run: |
           nextflow run . -profile test_tool,docker --verbose --tools ${{ matrix.tool }}

.travis.yml

@@ -14,7 +14,7 @@ before_install:
   - docker pull nfcore/sarek:dev
   # Fake the tag locally so that the pipeline runs properly
   # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1)
-  - docker tag nfcore/sarek:dev nfcore/sarek:2.5.2
+  - docker tag nfcore/sarek:dev nfcore/sarek:dev
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -4,6 +4,10 @@ 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).
 
+## dev
+
+- [#80](https://github.com/nf-core/sarek/pull/80) - Re-bump `dev` branch
+
 ## [2.5.2] - Jåkkåtjkaskajekna
 
 Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.

Dockerfile

@@ -4,4 +4,4 @@ LABEL authors="Maxime Garcia, Szilveszter Juhos" \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/nf-core-sarek-2.5.2/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-dev/bin:$PATH

Jenkinsfile

@@ -9,11 +9,11 @@ pipeline {
         stage('Docker setup') {
             steps {
                  sh "docker pull nfcore/sarek:dev"
-                 sh "docker tag nfcore/sarek:dev nfcore/sarek:2.5.2"
+                 sh "docker tag nfcore/sarek:dev nfcore/sarek:dev"
                  sh "docker pull nfcore/sareksnpeff:dev.GRCh37"
-                 sh "docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:2.5.2.GRCh37"
+                 sh "docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:dev.GRCh37"
                  sh "docker pull nfcore/sarekvep:dev.GRCh37"
-                 sh "docker tag nfcore/sarekvep:dev.GRCh37 nfcore/sarekvep:2.5.2.GRCh37"
+                 sh "docker tag nfcore/sarekvep:dev.GRCh37 nfcore/sarekvep:dev.GRCh37"
             }
         }
         stage('Annotation') {

conf/base.config

@@ -65,11 +65,11 @@ process {
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withName:Snpeff {
-    container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:2.5.2' : "nfcore/sareksnpeff:2.5.2.${params.genome}"}
+    container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withLabel:VEP {
-    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:2.5.2' : "nfcore/sarekvep:2.5.2.${params.genome}"}
+    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:dev' : "nfcore/sarekvep:dev.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
 }

conf/test.config

@@ -24,11 +24,11 @@ params {
 
 process {
   withName:Snpeff {
-    container = 'nfcore/sareksnpeff:2.5.2.GRCh37'
+    container = 'nfcore/sareksnpeff:dev.GRCh37'
     maxForks = 1
   }
   withLabel:VEP {
-    container = 'nfcore/sarekvep:2.5.2.GRCh37'
+    container = 'nfcore/sarekvep:dev.GRCh37'
     maxForks = 1
   }
 }

containers/snpeff/Dockerfile

@@ -7,7 +7,7 @@ LABEL \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-snpeff-2.5.2/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-snpeff-dev/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38

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: sarek-snpeff-2.5.2
+name: sarek-snpeff-dev
 channels:
   - conda-forge
   - bioconda

containers/vep/Dockerfile

@@ -7,7 +7,7 @@ LABEL \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-vep-2.5.2/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-vep-dev/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38

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: sarek-vep-2.5.2
+name: sarek-vep-dev
 channels:
   - conda-forge
   - bioconda

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-2.5.2
+name: nf-core-sarek-dev
 channels:
   - conda-forge
   - bioconda

nextflow.config

@@ -87,7 +87,7 @@ params {
 // Container slug
 // Stable releases should specify release tag (ie: `2.5`)
 // Developmental code should specify dev
-process.container = 'nfcore/sarek:2.5.2'
+process.container = 'nfcore/sarek:dev'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -167,7 +167,7 @@ manifest {
   description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '2.5.2'
+  version = 'dev'
 }
 
 // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over