diff --git a/.circleci/config.yml b/.circleci/config.yml index ebce2b06eb..0af952fcb0 100644 --- a/.circleci/config.yml +++ b/.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 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 844d217b43..c178671d56 100644 --- a/.github/workflows/ci.yml +++ b/.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 ${{ matrix.tool }} diff --git a/.travis.yml b/.travis.yml index 1ee0bf40db..3713a63aff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,7 +14,7 @@ before_install: - docker pull nfcore/sarek:dev # Fake the tag locally so that the pipeline runs properly # Looks weird when this is :dev to :dev, but makes sense when testing code for a release (:dev to :1.0.1) - - docker tag nfcore/sarek:dev nfcore/sarek:2.5.2 + - docker tag nfcore/sarek:dev nfcore/sarek:dev install: # Install Nextflow diff --git a/CHANGELOG.md b/CHANGELOG.md index 1a6bfcaf79..3cdb1cc196 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). +## dev + +- [#80](https://github.com/nf-core/sarek/pull/80) - Re-bump `dev` branch + ## [2.5.2] - Jåkkåtjkaskajekna Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif. diff --git a/Dockerfile b/Dockerfile index 84d313d85a..3c10ce1729 100644 --- a/Dockerfile +++ b/Dockerfile @@ -4,4 +4,4 @@ LABEL authors="Maxime Garcia, Szilveszter Juhos" \ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/nf-core-sarek-2.5.2/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-sarek-dev/bin:$PATH diff --git a/Jenkinsfile b/Jenkinsfile index 71ea4d76b7..2a26fd3d5f 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -9,11 +9,11 @@ pipeline { stage('Docker setup') { steps { sh "docker pull nfcore/sarek:dev" - sh "docker tag nfcore/sarek:dev nfcore/sarek:2.5.2" + sh "docker tag nfcore/sarek:dev nfcore/sarek:dev" sh "docker pull nfcore/sareksnpeff:dev.GRCh37" - sh "docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:2.5.2.GRCh37" + sh "docker tag nfcore/sareksnpeff:dev.GRCh37 nfcore/sareksnpeff:dev.GRCh37" sh "docker pull nfcore/sarekvep:dev.GRCh37" - sh "docker tag nfcore/sarekvep:dev.GRCh37 nfcore/sarekvep:2.5.2.GRCh37" + sh "docker tag nfcore/sarekvep:dev.GRCh37 nfcore/sarekvep:dev.GRCh37" } } stage('Annotation') { diff --git a/conf/base.config b/conf/base.config index a21c748ba9..7c889b04ba 100644 --- a/conf/base.config +++ b/conf/base.config @@ -65,11 +65,11 @@ process { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } withName:Snpeff { - container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:2.5.2' : "nfcore/sareksnpeff:2.5.2.${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.${params.genome}"} errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } } diff --git a/conf/test.config b/conf/test.config index 55b2defe4d..d8b3673d9c 100644 --- a/conf/test.config +++ b/conf/test.config @@ -24,11 +24,11 @@ params { process { withName:Snpeff { - container = 'nfcore/sareksnpeff:2.5.2.GRCh37' + container = 'nfcore/sareksnpeff:dev.GRCh37' maxForks = 1 } withLabel:VEP { - container = 'nfcore/sarekvep:2.5.2.GRCh37' + container = 'nfcore/sarekvep:dev.GRCh37' maxForks = 1 } } diff --git a/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile index 65aea05046..d08854d769 100644 --- a/containers/snpeff/Dockerfile +++ b/containers/snpeff/Dockerfile @@ -7,7 +7,7 @@ LABEL \ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/sarek-snpeff-2.5.2/bin:$PATH +ENV PATH /opt/conda/envs/sarek-snpeff-dev/bin:$PATH # Setup default ARG variables ARG GENOME=GRCh38 diff --git a/containers/snpeff/environment.yml b/containers/snpeff/environment.yml index 35279d068c..e9b1f01e03 100644 --- a/containers/snpeff/environment.yml +++ b/containers/snpeff/environment.yml @@ -1,6 +1,6 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml -name: sarek-snpeff-2.5.2 +name: sarek-snpeff-dev channels: - conda-forge - bioconda diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile index 30d3ba5378..695e5ef865 100644 --- a/containers/vep/Dockerfile +++ b/containers/vep/Dockerfile @@ -7,7 +7,7 @@ LABEL \ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -ENV PATH /opt/conda/envs/sarek-vep-2.5.2/bin:$PATH +ENV PATH /opt/conda/envs/sarek-vep-dev/bin:$PATH # Setup default ARG variables ARG GENOME=GRCh38 diff --git a/containers/vep/environment.yml b/containers/vep/environment.yml index f5c437d330..d44a829ed8 100644 --- 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: sarek-vep-2.5.2 +name: sarek-vep-dev channels: - conda-forge - bioconda diff --git a/environment.yml b/environment.yml index 00a6acf06b..7b7b1bf897 100644 --- 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-sarek-2.5.2 +name: nf-core-sarek-dev channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 704668b631..674bad8460 100644 --- a/nextflow.config +++ b/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