Prepare release (#37)

maxulysse · web-flow · commit 24e460155d57 · 2019-09-20T10:34:05.000+02:00
* nf-core bump-version . 2.5
* add --skipQC all to ANNOTATE test
* update usage of download_image script
* update CHANGELOG
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -10,11 +10,11 @@ jobs:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sareksnpeff:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+          command: docker build -t nfcore/sareksnpeff:2.5.${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:dev.${GENOME}
+            docker push nfcore/sareksnpeff:2.5.${GENOME}
 
   snpeffgrch38:
     << : *buildsnpeff
@@ -45,10 +45,10 @@ jobs:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sarekvep:dev.${GENOME} containers/vep/. --build-arg GENOME=${GENOME} --build-arg SPECIES=${SPECIES} --build-arg VEP_VERSION=${VEP_VERSION}
+          command: docker build -t nfcore/sarekvep:2.5.${GENOME} containers/vep/. --build-arg GENOME=${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:dev.${GENOME}
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sarekvep:2.5.${GENOME}
 
   vepgrch38:
     << : *buildvep
diff --git a/.github/workflows/ci-extra.yml b/.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 --test ${{ matrix.test }}
+          ${GITHUB_WORKSPACE}/scripts/download_image.sh -n docker --source-version dev --target-version 2.5 --test ${{ matrix.test }}
       - name: Run test
         run: |
           ${GITHUB_WORKSPACE}/scripts/run_tests.sh --test ${{ matrix.test }} --verbose
diff --git 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:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:2.5
       - name: Run test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
diff --git 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:dev
+  - docker tag nfcore/sarek:dev nfcore/sarek:2.5
 
 install:
   # Install Nextflow
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,7 @@ 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).
 
-## Unreleased
+## [2.5] - Ålkatj
 
 Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.
 
@@ -90,6 +90,7 @@ Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/)
 - [#35](https://github.com/nf-core/sarek/pull/35) - Use `tabix` instead of `IGVtools` to build vcf indexes
 - [#35](https://github.com/nf-core/sarek/pull/35) - Refactor references handling
 - [#35](https://github.com/nf-core/sarek/pull/35) - use Channel values instead of `referenceMap`
+- [#37](https://github.com/nf-core/sarek/pull/37) - Bump version for Release
 
 ### `Removed`
 
diff --git 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-2.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-2.5/bin:$PATH
diff --git a/Jenkinsfile b/Jenkinsfile
@@ -8,7 +8,7 @@ pipeline {
     stages {
         stage('Docker setup') {
             steps {
-                 sh "./scripts/download_image.sh -n docker -t ALL -T dev -g smallGRCh37"
+                 sh "./scripts/download_image.sh -n docker -t ALL --source-version dev --target-version 2.5 -g smallGRCh37"
             }
         }
         stage('Germline') {
diff --git 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-2.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-snpeff-2.5/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
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: sarek-snpeff-2.5dev
+name: sarek-snpeff-2.5
 channels:
   - conda-forge
   - bioconda
diff --git 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-2.5dev/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-vep-2.5/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
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: sarek-vep-2.5dev
+name: sarek-vep-2.5
 channels:
   - conda-forge
   - bioconda
diff --git 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-2.5dev
+name: nf-core-sarek-2.5
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
@@ -86,7 +86,7 @@ params {
 
 // Container slug. Stable releases should specify release tag!
 // Developmental code should specify :dev
-process.container = 'nfcore/sarek:dev'
+process.container = 'nfcore/sarek:2.5'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -155,7 +155,7 @@ 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 = '2.5dev'
+  version = '2.5'
 }
 
 // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over
diff --git a/scripts/download_image.sh b/scripts/download_image.sh
@@ -3,13 +3,14 @@ set -xeuo pipefail
 
 # This script download and tag image for sarek tests
 
-usage() { echo "Usage: $0 <-t test|annotation tool> <-n engine> <-T version to pull/build> <-g genome>" 1>&2; exit 1; }
+usage() { echo "Usage: $0 <-t test|annotation tool> <-n engine> <-S version to pull/build> <-T version to tag> <-g genome>" 1>&2; exit 1; }
 
 ENGINE=docker
 GENOME=smallGRCh37
 NXF_SINGULARITY_CACHEDIR=${NXF_SINGULARITY_CACHEDIR:-work/singularity/.}
 TEST=ALL
 VERSION=dev
+TARGETVERSION=${VERSION}
 
 while [[ $# -gt 0 ]]
 do
@@ -25,7 +26,12 @@ do
     shift # past argument
     shift # past value
     ;;
-    -T|--tagged-version)
+    -T|--target-version)
+    TARGETVERSION=$2
+    shift # past argument
+    shift # past value
+    ;;
+    -S|--source-version)
     VERSION=$2
     shift # past argument
     shift # past value
@@ -66,15 +72,15 @@ get_image(){
 
 if [[ ALL,ANNOTATEBOTH,ANNOTATESNPEFF,SNPEFF =~ $TEST ]]
 then
-  get_image sareksnpeff ${VERSION}.${SOURCEGENOME} ${VERSION}.${GENOME}
+  get_image sareksnpeff ${VERSION}.${SOURCEGENOME} ${TARGETVERSION}.${GENOME}
 fi
 
 if [[ ALL,ANNOTATEBOTH,ANNOTATEVEP,VEP =~ $TEST ]]
 then
-  get_image sarekvep ${VERSION}.${SOURCEGENOME} ${VERSION}.${GENOME}
+  get_image sarekvep ${VERSION}.${SOURCEGENOME} ${TARGETVERSION}.${GENOME}
 fi
 
 if ! [[ ANNOTATEBOTH,ANNOTATESNPEFF,ANNOTATEVEP,LINT,SNPEFF,VEP =~ $TEST ]]
 then
-  get_image sarek ${VERSION} ${VERSION}
+  get_image sarek ${VERSION} ${TARGETVERSION}
 fi
diff --git a/scripts/run_tests.sh b/scripts/run_tests.sh
@@ -109,7 +109,7 @@ esac
 
 case $TEST in
   ANNOTATE)
-  run_sarek --step annotate --tools ${ANNOTATOR} --input ${PATHTOSAMPLE}/vcf/Strelka_1234N_variants.vcf.gz
+  run_sarek --step annotate --tools ${ANNOTATOR} --input ${PATHTOSAMPLE}/vcf/Strelka_1234N_variants.vcf.gz --skipQC all
   ;;
   GERMLINE)
   run_sarek --tools=false --input data/testdata/tiny/normal

Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@ pipeline {`
`8`	`8`	`stages {`
`9`	`9`	`stage('Docker setup') {`
`10`	`10`	`steps {`
`11`		`- sh "./scripts/download_image.sh -n docker -t ALL -T dev -g smallGRCh37"`
	`11`	`+ sh "./scripts/download_image.sh -n docker -t ALL --source-version dev --target-version 2.5 -g smallGRCh37"`
`12`	`12`	`}`
`13`	`13`	`}`
`14`	`14`	`stage('Germline') {`