Merge pull request #53 from MaxUlysse/patch

Prepare release 2.5.1

.circleci/config.yml

@@ -10,11 +10,11 @@ jobs:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sareksnpeff:2.5.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+          command: docker build -t nfcore/sareksnpeff:2.5.1.${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.${GENOME}
+            docker push nfcore/sareksnpeff:2.5.1.${GENOME}
 
   snpeffgrch38:
     << : *buildsnpeff
@@ -45,10 +45,10 @@ jobs:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sarekvep:2.5.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          command: docker build -t nfcore/sarekvep:2.5.1.${GENOME} containers/vep/. --build-arg GENOME=${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.${GENOME}
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:2.5.1.${GENOME}
 
   vepgrch38:
     << : *buildvep

.github/workflows/branch.yml

@@ -13,4 +13,4 @@ jobs:
       - uses: actions/checkout@v1
       - name: Check PRs
         run: |
-          [[ $(git remote get-url origin) == *nf-core/sarek ]] && [ ${GITHUB_BASE_REF} = "master" ] && [ ${GITHUB_HEAD_REF} = "dev" ]
+          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == patch* ]]

.github/workflows/ci-extra.yml

@@ -18,7 +18,7 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Download image
         run: |
-          ${GITHUB_WORKSPACE}/scripts/download_image.sh -n docker --source-version dev --target-version 2.5 --test ${{ matrix.test }}
+          ${GITHUB_WORKSPACE}/scripts/download_image.sh -n docker --source-version 2.5 --target-version 2.5.1 --test ${{ matrix.test }}
       - name: Run test
         run: |
           ${GITHUB_WORKSPACE}/scripts/run_tests.sh --test ${{ matrix.test }} --verbose

.github/workflows/ci.yml

@@ -17,8 +17,8 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Download and tag image
         run: |
-          docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:2.5
+          docker pull nfcore/sarek:2.5
+          docker tag nfcore/sarek:2.5 nfcore/sarek:2.5.1
       - name: Run test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker

.travis.yml

@@ -9,12 +9,12 @@ matrix:
 
 before_install:
   # PRs to master are only ok if coming from dev branch
-  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && ([ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ] || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]))'
+  - '[ $TRAVIS_PULL_REQUEST = "false" ] || [ $TRAVIS_BRANCH != "master" ] || ([ $TRAVIS_PULL_REQUEST_SLUG = $TRAVIS_REPO_SLUG ] && [ $TRAVIS_PULL_REQUEST_BRANCH = "dev" ]) || [ $TRAVIS_PULL_REQUEST_BRANCH = "patch" ]'
   # Pull the docker image first so the test doesn't wait for this
   - 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
+  - docker tag nfcore/sarek:dev nfcore/sarek:2.5.1
 
 install:
   # Install Nextflow

CHANGELOG.md

@@ -5,6 +5,16 @@ 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).
 
+## [2.5.1] - Årjep-Ålkatjjekna
+
+Årjep-Ålkatjjekna is one of the two glaciers of the Ålkatj Massif.
+
+### `Fixed`
+
+- [#48](https://github.com/nf-core/sarek/issues/48) - Fix `singularity.autoMounts` issue.
+- [#49](https://github.com/nf-core/sarek/issues/49) - Use correct tag for annotation containers.
+- [#50](https://github.com/nf-core/sarek/issues/50) - Fix paths for scripts.
+
 ## [2.5] - Ålkatj
 
 Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.

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/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-2.5.1/bin:$PATH

Jenkinsfile

@@ -8,7 +8,7 @@ pipeline {
     stages {
         stage('Docker setup') {
             steps {
-                 sh "./scripts/download_image.sh -n docker -t ALL --source-version dev --target-version 2.5 -g smallGRCh37"
+                 sh "./scripts/download_image.sh -n docker -t ALL --source-version 2.5 --target-version 2.5.1 -g smallGRCh37"
             }
         }
         stage('Germline') {

README.md

@@ -98,7 +98,7 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 If you use nf-core/sarek for your analysis, please cite the `Sarek` pre-print as follows:
 > Garcia MU, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, de Ståhl TD, Wirta V, Nistér M, Nystedt B, Käller M. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants**. *bioRxiv*. 2018. p. 316976. [doi: 10.1101/316976](https://www.biorxiv.org/content/10.1101/316976v1).
 
-You can cite the sarek zenodo record for a specific version using the following [DOI: 10.5281/zenodo.3476426 ](https://zenodo.org/badge/latestdoi/184289291)
+You can cite the sarek zenodo record for a specific version using the following [doi: 10.5281/zenodo.3476426](https://zenodo.org/badge/latestdoi/184289291)
 
 You can cite the `nf-core` pre-print as follows:
 > Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. **nf-core: Community curated bioinformatics pipelines**. *bioRxiv*. 2019. p. 610741. [doi: 10.1101/610741](https://www.biorxiv.org/content/10.1101/610741v3).

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.${params.genome}"}
+    container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:2.5.1' : "nfcore/sareksnpeff:2.5.1.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withLabel:VEP {
-    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:dev' : "nfcore/sarekvep:dev.${params.genome}"}
+    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:2.5.1' : "nfcore/sarekvep:2.5.1.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
 }

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/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-snpeff-2.5.1/bin:$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
+name: sarek-snpeff-2.5.1
 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/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-vep-2.5.1/bin:$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
+name: sarek-vep-2.5.1
 channels:
   - conda-forge
   - bioconda

docs/annotation.md

@@ -63,7 +63,7 @@ An helper script has been designed to help downloading CADD files.
 Such files are meant to be share between multiple users, so this script is mainly meant for people administrating servers, clusters and advanced users.
 
 ```bash
-nextflow run build.nf --cadd_cache /Path/To/CADDcache --cadd_version <CADD version> --genome <GENOME>
+nextflow run downloadcache.nf --cadd_cache /Path/To/CADDcache --cadd_version <CADD version> --genome <GENOME>
 ```
 
 ## Using VEP GeneSplicer plugin

docs/install_bianca.md

@@ -92,10 +92,10 @@ You can either download nf-core/sarek on your computer or on `rackham`, make an
 > pip install git-archive-all
 # If you used --user before, you might want to do that here too
 > pip install git-archive-all --user
-> ./scripts/makeSnapshot.sh --include-test-data --include-configs
+> ./scripts/make_snapshot.sh --include-test-data --include-configs
 
 # Or you can just include nf-core/sarek:
-> ./scripts/makeSnapshot.sh
+> ./scripts/make_snapshot.sh
 
 # You will get this message in your terminal
 Wrote sarek-[snapID].tar.gz

docs/reference.md

@@ -36,11 +36,3 @@ First, when there are multiple consecutive intervals in the file that take littl
 Second, the jobs with largest processing time are started first, which reduces wall-clock time.
 If no runtime is given, a time of 1000 nucleotides per second is assumed.
 Actual figures vary from 2 nucleotides/second to 30000 nucleotides/second.
-
-## build.nf
-
-The [`build.nf`](#buildnf) script is used to build reference needed for smallGRCh37.
-
-```bash
-nextflow run build.nf
-```

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
+name: nf-core-sarek-2.5.1
 channels:
   - conda-forge
   - bioconda

main.nf

@@ -1983,12 +1983,12 @@ process ControlFreecViz {
     when: 'controlfreec' in tools
 
     """
-    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}
-    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvNormal} ${ratioNormal}
-    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
-    cat /opt/conda/envs/sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioNormal} ${bafNormal}
-    perl /opt/conda/envs/sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioTumor} > ${idSampleTumor}.bed
-    perl /opt/conda/envs/sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioNormal} > ${idSampleNormal}.bed
+    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvTumor} ${ratioTumor}
+    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/assess_significance.R | R --slave --args ${cnvNormal} ${ratioNormal}
+    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioTumor} ${bafTumor}
+    cat /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/makeGraph.R | R --slave --args 2 ${ratioNormal} ${bafNormal}
+    perl /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioTumor} > ${idSampleTumor}.bed
+    perl /opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/freec2bed.pl -f ${ratioNormal} > ${idSampleNormal}.bed
     """
 }
 
@@ -2249,7 +2249,7 @@ process VEP {
     genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
     dir_cache = (params.vep_cache && params.annotation_cache) ? " \${PWD}/${dataDir}" : "/.vep"
     cadd = (params.cadd_cache && params.cadd_WG_SNVs && params.cadd_InDels) ? "--plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz" : ""
-    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
+    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
     """
     mkdir ${reducedVCF}
 
@@ -2310,7 +2310,7 @@ process VEPmerge {
     genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
     dir_cache = (params.vep_cache && params.annotation_cache) ? " \${PWD}/${dataDir}" : "/.vep"
     cadd = (params.cadd_cache && params.cadd_WG_SNVs && params.cadd_InDels) ? "--plugin CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz" : ""
-    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
+    genesplicer = params.genesplicer ? "--plugin GeneSplicer,/opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/bin/genesplicer,/opt/conda/envs/nf-core-sarek-${workflow.manifest.version}/share/genesplicer-1.0-1/human,context=200,tmpdir=\$PWD/${reducedVCF}" : "--offline"
     """
     mkdir ${reducedVCF}
 

nextflow.config

@@ -86,7 +86,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/sarek:2.5'
+process.container = 'nfcore/sarek:2.5.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -115,8 +115,8 @@ profiles {
     singularity.enabled = false
   }
   singularity {
-    autoMounts = true
     docker.enabled = false
+    singularity.autoMounts = true
     singularity.enabled = true
   }
   test { includeConfig 'conf/test.config' }
@@ -156,7 +156,7 @@ manifest {
   description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.04.0'
-  version = '2.5'
+  version = '2.5.1'
 }
 
 // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over

scripts/download_image.sh

@@ -80,7 +80,4 @@ then
   get_image sarekvep ${VERSION}.${SOURCEGENOME} ${TARGETVERSION}.${GENOME}
 fi
 
-if ! [[ ANNOTATEBOTH,ANNOTATESNPEFF,ANNOTATEVEP,LINT,SNPEFF,VEP =~ $TEST ]]
-then
-  get_image sarek ${VERSION} ${TARGETVERSION}
-fi
+get_image sarek ${VERSION} ${TARGETVERSION}