From 0ce68020f7b62288cce61b1c3df252afa911cc0a Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 26 Jan 2021 14:44:39 +0100 Subject: [PATCH 01/66] chores: merge 2.7 to dev --- .circleci/config.yml | 20 ++++++++++---------- .github/workflows/ci.yml | 18 +++++++++--------- CHANGELOG.md | 2 ++ Dockerfile | 4 ++-- conf/base.config | 4 ++-- conf/test.config | 4 ++-- containers/snpeff/Dockerfile | 4 ++-- containers/snpeff/environment.yml | 2 +- containers/vep/Dockerfile | 4 ++-- containers/vep/environment.yml | 2 +- environment.yml | 2 +- nextflow.config | 4 ++-- 12 files changed, 36 insertions(+), 34 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 39353df167..216b0cd8c5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -6,7 +6,7 @@ jobs: environment: GENOME: GRCh37 SNPEFF_CACHE_VERSION: "75" - SAREK_TAG: 2.7 + SAREK_TAG: dev steps: - checkout - setup_remote_docker @@ -20,28 +20,28 @@ jobs: environment: GENOME: GRCh38 SNPEFF_CACHE_VERSION: "86" - SAREK_TAG: 2.7 + SAREK_TAG: dev snpeffgrcm38: << : *buildsnpeff environment: GENOME: GRCm38 SNPEFF_CACHE_VERSION: "86" - SAREK_TAG: 2.7 + SAREK_TAG: dev snpeffcanfam3_1: << : *buildsnpeff environment: GENOME: CanFam3.1 SNPEFF_CACHE_VERSION: "86" - SAREK_TAG: 2.7 + SAREK_TAG: dev snpeffwbcel235: << : *buildsnpeff environment: GENOME: WBcel235 SNPEFF_CACHE_VERSION: "86" - SAREK_TAG: 2.7 + SAREK_TAG: dev vepgrch37: &buildvep docker: @@ -50,7 +50,7 @@ jobs: GENOME: GRCh37 SPECIES: homo_sapiens VEP_VERSION: "99" - SAREK_TAG: 2.7 + SAREK_TAG: dev steps: - checkout - setup_remote_docker @@ -67,7 +67,7 @@ jobs: GENOME: GRCh38 SPECIES: homo_sapiens VEP_VERSION: "99" - SAREK_TAG: 2.7 + SAREK_TAG: dev vepgrcm38: << : *buildvep @@ -75,7 +75,7 @@ jobs: GENOME: GRCm38 SPECIES: mus_musculus VEP_VERSION: "99" - SAREK_TAG: 2.7 + SAREK_TAG: dev vepcanfam3_1: << : *buildvep @@ -83,7 +83,7 @@ jobs: GENOME: CanFam3.1 SPECIES: canis_familiaris VEP_VERSION: "99" - SAREK_TAG: 2.7 + SAREK_TAG: dev vepwbcel235: << : *buildvep @@ -91,7 +91,7 @@ jobs: GENOME: WBcel235 SPECIES: caenorhabditis_elegans VEP_VERSION: "99" - SAREK_TAG: 2.7 + SAREK_TAG: dev workflows: version: 2 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index db0273fb2a..83dee22c5e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,13 +33,13 @@ jobs: environment.yml - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t nfcore/sarek:2.7 + run: docker build --no-cache . -t nfcore/sarek:dev - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull nfcore/sarek:dev - docker tag nfcore/sarek:dev nfcore/sarek:2.7 + docker tag nfcore/sarek:dev nfcore/sarek:dev - name: Install Nextflow env: @@ -71,8 +71,8 @@ jobs: NXF_VER: '20.04.0' - name: Pull docker image run: | - docker pull nfcore/sarek:2.7 - docker pull nfcore/sarek${{ matrix.tools }}:2.7.${{ matrix.species }} + docker pull nfcore/sarek:dev + docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }} - name: Run annotation test run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }} @@ -93,7 +93,7 @@ jobs: # Only check Nextflow pipeline minimum version NXF_VER: '20.04.0' - name: Pull docker image - run: docker pull nfcore/sarek:2.7 + run: docker pull nfcore/sarek:dev - name: Get test data run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data - name: Run germline test @@ -121,7 +121,7 @@ jobs: # Only check Nextflow pipeline minimum version NXF_VER: '20.04.0' - name: Pull docker image - run: docker pull nfcore/sarek:2.7 + run: docker pull nfcore/sarek:dev - 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 @@ -142,7 +142,7 @@ jobs: # Only check Nextflow pipeline minimum version NXF_VER: '20.04.0' - name: Pull docker image - run: docker pull nfcore/sarek:2.7 + run: docker pull nfcore/sarek:dev - name: Run ${{ matrix.profile }} test run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker @@ -163,7 +163,7 @@ jobs: # Only check Nextflow pipeline minimum version NXF_VER: '20.04.0' - name: Pull docker image - run: docker pull nfcore/sarek:2.7 + run: docker pull nfcore/sarek:dev - name: Run ${{ matrix.profile }} test run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }} @@ -194,6 +194,6 @@ jobs: # Only check Nextflow pipeline minimum version NXF_VER: '20.04.0' - name: Pull docker image - run: docker pull nfcore/sarek:2.7 + run: docker pull nfcore/sarek:dev - name: Run ${{ matrix.tool }} test run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }} diff --git a/CHANGELOG.md b/CHANGELOG.md index 3db854e7a0..98a20791b6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,8 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## dev + ## [2.7](https://github.com/nf-core/sarek/releases/tag/2.7) - Pårte Pårte is one of the main massif in the Sarek National Park. diff --git a/Dockerfile b/Dockerfile index 7531851725..dbdec87e1c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,10 +7,10 @@ COPY environment.yml / RUN conda env create --quiet -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-sarek-2.7/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-sarek-3.0dev/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-sarek-2.7 > nf-core-sarek-2.7.yml +RUN conda env export --name nf-core-sarek-3.0dev > nf-core-sarek-3.0dev.yml # Instruct R processes to use these empty files instead of clashing with a local version RUN touch .Rprofile diff --git a/conf/base.config b/conf/base.config index c7392fdf62..ac13fe4927 100644 --- a/conf/base.config +++ b/conf/base.config @@ -90,11 +90,11 @@ process { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } withName:Snpeff { - container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7' : "nfcore/sareksnpeff:2.7.${params.genome}"} + container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"} errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } withLabel:VEP { - container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:2.7' : "nfcore/sarekvep:2.7.${params.genome}"} + container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:dev' : "nfcore/sarekvep:dev.${params.genome}"} errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } } diff --git a/conf/test.config b/conf/test.config index f7313e34b9..50f523c9b2 100644 --- a/conf/test.config +++ b/conf/test.config @@ -30,11 +30,11 @@ params { process { withName:Snpeff { - container = 'nfcore/sareksnpeff:2.7.WBcel235' + container = 'nfcore/sareksnpeff:dev.WBcel235' maxForks = 1 } withLabel:VEP { - container = 'nfcore/sarekvep:2.7.WBcel235' + container = 'nfcore/sarekvep:dev.WBcel235' maxForks = 1 } } diff --git a/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile index dac706400c..6af8b3f089 100644 --- a/containers/snpeff/Dockerfile +++ b/containers/snpeff/Dockerfile @@ -9,7 +9,7 @@ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-sarek-snpeff-2.7/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-sarek-snpeff-dev/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-2.7 > nf-core-sarek-snpeff-2.7.yml +RUN conda env export --name nf-core-sarek-snpeff-dev > nf-core-sarek-snpeff-dev.yml diff --git a/containers/snpeff/environment.yml b/containers/snpeff/environment.yml index 29e2a0d40f..424e23e305 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: nf-core-sarek-snpeff-2.7 +name: nf-core-sarek-snpeff-dev channels: - conda-forge - bioconda diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile index 6f0e927ce6..d34936609e 100644 --- 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-2.7/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-sarek-vep-dev/bin:$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-2.7 > nf-core-sarek-vep-2.7.yml +RUN conda env export --name nf-core-sarek-vep-dev > nf-core-sarek-vep-dev.yml diff --git a/containers/vep/environment.yml b/containers/vep/environment.yml index 701a70b561..e90fff10e5 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: nf-core-sarek-vep-2.7 +name: nf-core-sarek-vep-dev channels: - conda-forge - bioconda diff --git a/environment.yml b/environment.yml index 7a8820949f..730b0674cd 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-2.7 +name: nf-core-sarek-3.0dev channels: - conda-forge - bioconda diff --git a/nextflow.config b/nextflow.config index 52a93501b8..fd0755e56f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -107,7 +107,7 @@ params { // Container slug // Stable releases should specify release tag (ie: `2.5.2`) // Developmental code should specify dev -process.container = 'nfcore/sarek:2.7' +process.container = 'nfcore/sarek:dev' // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -199,7 +199,7 @@ manifest { description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing' mainScript = 'main.nf' nextflowVersion = '>=20.04.0' - version = '2.7' + version = '3.0dev' } // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over From d56135d1e6a79cf05d61467a5286d8a031c97270 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 26 Jan 2021 16:35:37 +0100 Subject: [PATCH 02/66] chores: remove extra head tag --- assets/email_template.html | 1 - 1 file changed, 1 deletion(-) diff --git a/assets/email_template.html b/assets/email_template.html index 1d069c4254..36a9983efd 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,6 +1,5 @@ - From 31c43f296ca4db3499ba0c5132e80fd90e1c6231 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 26 Jan 2021 16:39:50 +0100 Subject: [PATCH 03/66] fix: remove conflicts comments --- docs/images/sarek_workflow.svg | 28 ---------------------------- 1 file changed, 28 deletions(-) diff --git a/docs/images/sarek_workflow.svg b/docs/images/sarek_workflow.svg index 3878728c35..6fcf577a58 100644 --- a/docs/images/sarek_workflow.svg +++ b/docs/images/sarek_workflow.svg @@ -2177,10 +2177,6 @@ y="-2749.4028" x="866.00854" /> -<<<<<<< HEAD -======= - 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