From 555ad7ad698bb5ae5dc9ffe8ab6b6623c7592cd0 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Wed, 18 Sep 2019 15:46:28 +0200
Subject: [PATCH 1/9] nf-core bump-version . 2.5

---
 .travis.yml                       | 2 +-
 CHANGELOG.md                      | 2 +-
 Dockerfile                        | 2 +-
 containers/snpeff/Dockerfile      | 2 +-
 containers/snpeff/environment.yml | 2 +-
 containers/vep/Dockerfile         | 2 +-
 containers/vep/environment.yml    | 2 +-
 environment.yml                   | 2 +-
 nextflow.config                   | 4 ++--
 9 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index e2d4b23d67..f34465aad6 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:dev
+  - docker tag nfcore/sarek:dev nfcore/sarek:2.5
 
 install:
   # Install Nextflow
diff --git a/CHANGELOG.md b/CHANGELOG.md
index ca2d3eb1fb..ad5590b8fa 100644
--- 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 - 2019-09-XX
 
 Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.
 
diff --git a/Dockerfile b/Dockerfile
index 8cb51fe468..a1b6fda1c6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,4 +4,4 @@ LABEL authors="Maxime Garcia" \
 
 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/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile
index 08b47c22b7..07ccb28152 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-2.5dev/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
index 5e48bdb781..fd93bd1815 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-2.5dev
+name: sarek-snpeff-2.5
 channels:
   - conda-forge
   - bioconda
diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile
index 06c12a7bb8..7969b5d1e7 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-2.5dev/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
index 5fd86c3cdc..b5c73474a6 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-2.5dev
+name: sarek-vep-2.5
 channels:
   - conda-forge
   - bioconda
diff --git a/environment.yml b/environment.yml
index 683facbebb..2ae3303c97 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-2.5dev
+name: nf-core-sarek-2.5
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
index ec1ca9b05c..f0ae184de0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -36,7 +36,7 @@ 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'
@@ -105,7 +105,7 @@ 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

From 420101aef35eea66b93f8302203c75aefc947c6b Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 19 Sep 2019 09:58:14 +0200
Subject: [PATCH 2/9] update version for images as well

---
 .circleci/config.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 0af952fcb0..1ede7ab8fe 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: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

From faa0d16eeeea0057afd860f21a6582c347a1092d Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 19 Sep 2019 10:13:33 +0200
Subject: [PATCH 3/9] fix CI

---
 .github/workflows/ci.yml  |  2 +-
 scripts/download_image.sh | 15 +++++++++++----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 22c1031208..785fb9269c 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:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:2.5
       - name: Run test
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker
\ No newline at end of file
diff --git a/scripts/download_image.sh b/scripts/download_image.sh
index 959e8fb843..9f3e1a62d9 100755
--- 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> <-T version to pull/build> <-a 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=2.5
 
 while [[ $# -gt 0 ]]
 do
@@ -25,6 +26,11 @@ do
     shift # past argument
     shift # past value
     ;;
+    -a|--target-version)
+    TARGETVERSION=$2
+    shift # past argument
+    shift # past value
+    ;;
     -T|--tagged-version)
     VERSION=$2
     shift # past argument
@@ -43,6 +49,7 @@ do
 done
 
 SOURCEGENOME=${GENOME}
+TARGETVERSION=${VERSION}
 
 if [[ smallGRCh37 =~ $SOURCEGENOME ]]
 then
@@ -66,15 +73,15 @@ 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

From dfca662cd66b5322f32ece4aa0a95073a6f059a1 Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Thu, 19 Sep 2019 14:04:11 +0200
Subject: [PATCH 4/9] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ad5590b8fa..b78ec5dbee 100644
--- 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).
 
-## [2.5] - Ålkatj - 2019-09-XX
+## [2.5] - Ålkatj
 
 Initial release of `nf-core/sarek`, created with the [nf-core](http://nf-co.re/) template.
 

From da4706e42b449711eb2f67f357f29f26918cbd81 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 19 Sep 2019 15:37:34 +0200
Subject: [PATCH 5/9] fix tag for containers

---
 scripts/download_image.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/scripts/download_image.sh b/scripts/download_image.sh
index 9f3e1a62d9..58227d7935 100755
--- a/scripts/download_image.sh
+++ b/scripts/download_image.sh
@@ -10,7 +10,7 @@ GENOME=smallGRCh37
 NXF_SINGULARITY_CACHEDIR=${NXF_SINGULARITY_CACHEDIR:-work/singularity/.}
 TEST=ALL
 VERSION=dev
-TARGETVERSION=2.5
+TARGETVERSION=${VERSION}
 
 while [[ $# -gt 0 ]]
 do
@@ -49,7 +49,6 @@ do
 done
 
 SOURCEGENOME=${GENOME}
-TARGETVERSION=${VERSION}
 
 if [[ smallGRCh37 =~ $SOURCEGENOME ]]
 then

From 97dbb692c9e275231e353b8938677dfab3881724 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 19 Sep 2019 15:44:05 +0200
Subject: [PATCH 6/9] actually using the right arg in the script...

---
 .github/workflows/ci-extra.yml | 2 +-
 scripts/download_image.sh      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/ci-extra.yml b/.github/workflows/ci-extra.yml
index cfd23ca890..90543c7958 100644
--- 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
\ No newline at end of file
diff --git a/scripts/download_image.sh b/scripts/download_image.sh
index 58227d7935..00892c09b3 100755
--- a/scripts/download_image.sh
+++ b/scripts/download_image.sh
@@ -3,7 +3,7 @@ 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> <-a version to tag> <-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
@@ -26,12 +26,12 @@ do
     shift # past argument
     shift # past value
     ;;
-    -a|--target-version)
+    -T|--target-version)
     TARGETVERSION=$2
     shift # past argument
     shift # past value
     ;;
-    -T|--tagged-version)
+    -S|--source-version)
     VERSION=$2
     shift # past argument
     shift # past value

From d21f257bc750aef87f169073ee0d89b5500a537b Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Sep 2019 09:34:20 +0200
Subject: [PATCH 7/9] add --skipQC all to ANNOTATE test

---
 scripts/run_tests.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/run_tests.sh b/scripts/run_tests.sh
index d79a821913..cb6db88901 100755
--- 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

From f4a2baf0e29046da2fbe0031219b1f36a2d51c6b Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Sep 2019 09:42:41 +0200
Subject: [PATCH 8/9] update usage of download_image script

---
 Jenkinsfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Jenkinsfile b/Jenkinsfile
index a48cedb877..924e454f0d 100644
--- 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') {

From dbd49f15a9555fdb54c5e4a2ab0f9885debae633 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Fri, 20 Sep 2019 10:07:58 +0200
Subject: [PATCH 9/9] update CHANGELOG

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b78ec5dbee..8adbcab63a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -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`