From 81485467b51a6616c86467284b813151046fcc45 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 14:25:22 +0200
Subject: [PATCH 01/23] nf-core bump-version . 2.5.1

---
 .travis.yml     | 2 +-
 Dockerfile      | 2 +-
 environment.yml | 2 +-
 nextflow.config | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3598ccf284..e08837e8fc 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
+  - docker tag nfcore/sarek:dev nfcore/sarek:2.5.1
 
 install:
   # Install Nextflow
diff --git a/Dockerfile b/Dockerfile
index c012a49d05..c493eab98f 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/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-2.5.1/bin:$PATH
diff --git a/environment.yml b/environment.yml
index 2ae3303c97..c27f23966a 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
+name: nf-core-sarek-2.5.1
 channels:
   - conda-forge
   - bioconda
diff --git a/nextflow.config b/nextflow.config
index 852831b8e4..d9aa514c8d 100644
--- 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:2.5'
+process.container = 'nfcore/sarek:2.5.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.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

From e3453c686d83d0f0d8bd070e1b1ad07e53eb2e5c Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 14:26:23 +0200
Subject: [PATCH 02/23] fix script name in docs

---
 docs/install_bianca.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/install_bianca.md b/docs/install_bianca.md
index 5bb8c176c8..6cc0b51960 100644
--- a/docs/install_bianca.md
+++ b/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

From 6aa109130e72fd51b71c46f5ca6032366aab16ef Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 14:27:49 +0200
Subject: [PATCH 03/23] fix markdownlint

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

diff --git a/README.md b/README.md
index 10e2544ca6..8460be05c9 100644
--- a/README.md
+++ b/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).

From 33ff41fb77e66522ac20beb8eef0da7e467cc20a Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 14:28:42 +0200
Subject: [PATCH 04/23] fix autoMounts in singularity profile, closes #48

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index d9aa514c8d..66b9397593 100644
--- a/nextflow.config
+++ b/nextflow.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' }

From a7b0f0002d7136cac96d8b5740e475fd257d24fd Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 14:30:23 +0200
Subject: [PATCH 05/23] fix path to script, close #50

---
 main.nf | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/main.nf b/main.nf
index ffe3b12b7d..204f315b4d 100644
--- a/main.nf
+++ b/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}
 

From a3e45c6e046589b38e283c6bab1a30a20d9959d4 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 15:33:01 +0200
Subject: [PATCH 06/23] build 2.5.1 version of annotation containers

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

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1ede7ab8fe..2da763cf15 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.${GENOME} containers/snpeff/. --build-arg GENOME=${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

From d00a8f7b531f8f22adbb4b84693571b880263997 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 15:33:29 +0200
Subject: [PATCH 07/23] add patch to branch protection

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 58a41ff689..054d2d78f2 100644
--- a/.github/workflows/branch.yml
+++ b/.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_BASE_REF} = "patch" ]]; }
\ No newline at end of file

From 8dfc48ace72a59e0c93bd4cf9367ef72912e90c4 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 15:35:28 +0200
Subject: [PATCH 08/23] pull image 2.5,tag it as 2.5.1

---
 .github/workflows/ci-extra.yml | 2 +-
 .github/workflows/ci.yml       | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/ci-extra.yml b/.github/workflows/ci-extra.yml
index 040dc11ffe..442be114bb 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 --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
\ No newline at end of file
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 785fb9269c..16fc90d4d1 100644
--- a/.github/workflows/ci.yml
+++ b/.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
\ No newline at end of file

From db4775c2cd067a82745bae9f64d65bc7f2e8a98c Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 16:29:34 +0200
Subject: [PATCH 09/23] pull image 2.5,tag it as 2.5.1

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

diff --git a/Jenkinsfile b/Jenkinsfile
index 924e454f0d..ffe06115b0 100644
--- a/Jenkinsfile
+++ b/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') {

From 642ddfb72eb28317f1a679f2e2eacb9ff68cc859 Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 16:30:21 +0200
Subject: [PATCH 10/23] use correct tag for containers close #49

---
 conf/base.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/base.config b/conf/base.config
index 5c76d275e6..4e46501b14 100644
--- a/conf/base.config
+++ b/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'}
   }
 }

From 94c82e221a3f21d6fd54cd0a643f482adc41b31f Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 16:32:18 +0200
Subject: [PATCH 11/23] bump version to 2.5.1

---
 containers/snpeff/Dockerfile      | 2 +-
 containers/snpeff/environment.yml | 2 +-
 containers/vep/Dockerfile         | 2 +-
 containers/vep/environment.yml    | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/containers/snpeff/Dockerfile b/containers/snpeff/Dockerfile
index 3ac9b89dd7..769ef317e9 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/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-snpeff-2.5.1/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
diff --git a/containers/snpeff/environment.yml b/containers/snpeff/environment.yml
index fd93bd1815..31428bb7a4 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
+name: sarek-snpeff-2.5.1
 channels:
   - conda-forge
   - bioconda
diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile
index cfe2d8eeb5..e140f8e77b 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/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-vep-2.5.1/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
diff --git a/containers/vep/environment.yml b/containers/vep/environment.yml
index b5c73474a6..b1d32f1d02 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
+name: sarek-vep-2.5.1
 channels:
   - conda-forge
   - bioconda

From c650e080f69d0f77f820243233690cf2bbb8bcae Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 16:32:39 +0200
Subject: [PATCH 12/23] update script name

---
 docs/annotation.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/annotation.md b/docs/annotation.md
index 8e426e2140..b7babedc7c 100644
--- a/docs/annotation.md
+++ b/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

From 424a4f534040caed2bad6c0d70eb09426f7b51bf Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 16:33:42 +0200
Subject: [PATCH 13/23] update docs

---
 docs/reference.md | 8 --------
 1 file changed, 8 deletions(-)

diff --git a/docs/reference.md b/docs/reference.md
index 1d5d10c729..9e69e2dcdd 100644
--- a/docs/reference.md
+++ b/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
-```

From 8ba3e47d9c6f1044b8eb42de13240c073ff6941a Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 16:53:46 +0200
Subject: [PATCH 14/23] update CHANGELOG

---
 CHANGELOG.md | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 080ba18d72..e35bf7ad3c 100644
--- a/CHANGELOG.md
+++ b/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.

From 84f039c9658e3cc70be23b71a16a702be02b674e Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Mon, 21 Oct 2019 17:18:40 +0200
Subject: [PATCH 15/23] always download nfcore/sarek

---
 scripts/download_image.sh | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/scripts/download_image.sh b/scripts/download_image.sh
index 00892c09b3..730e8fe945 100755
--- a/scripts/download_image.sh
+++ b/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}

From b238dd6ed1f1b4ed47578c0c847fdba6bee8c615 Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 10:57:19 +0200
Subject: [PATCH 16/23] Try to fix branch protection

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 054d2d78f2..8cbf3d1546 100644
--- a/.github/workflows/branch.yml
+++ b/.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" ]] || [[ ${GITHUB_BASE_REF} = "patch" ]]; }
\ No newline at end of file
+          [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]] || [[ ${GITHUB_BASE_REF} = "patch" ]]

From 83e5348934b9949c473a22ec7c9c9432ab075ec6 Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 10:59:47 +0200
Subject: [PATCH 17/23] Group checks

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 8cbf3d1546..75836dd0a0 100644
--- a/.github/workflows/branch.yml
+++ b/.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" ]] || [[ ${GITHUB_BASE_REF} = "patch" ]]
+          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]] ; } || [[ ${GITHUB_BASE_REF} = "patch" ]]

From 114e2c0a0b58ac12162008a0e1ff6b258a23ce54 Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 11:12:36 +0200
Subject: [PATCH 18/23] rewrote test

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 75836dd0a0..3247c86312 100644
--- a/.github/workflows/branch.yml
+++ b/.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" ]] ; } || [[ ${GITHUB_BASE_REF} = "patch" ]]
+         [[ ${GITHUB_HEAD_REF} = "patch" ]] || [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]

From b76f217ad2f504433252270420cd896ecdbdbedf Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 11:23:39 +0200
Subject: [PATCH 19/23] This time it'll work

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 3247c86312..5a51271ef7 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,4 +13,4 @@ jobs:
       - uses: actions/checkout@v1
       - name: Check PRs
         run: |
-         [[ ${GITHUB_HEAD_REF} = "patch" ]] || [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]
+         [[ ${GITHUB_HEAD_REF} = "patch" ]] || { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]] }```

From 67bc3410974e1f18b20ca04d5aa03112c3e20aed Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 11:25:30 +0200
Subject: [PATCH 20/23] Typo

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 5a51271ef7..431dae2e52 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,4 +13,4 @@ jobs:
       - uses: actions/checkout@v1
       - name: Check PRs
         run: |
-         [[ ${GITHUB_HEAD_REF} = "patch" ]] || { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]] }```
+         [[ ${GITHUB_HEAD_REF} = "patch" ]] || { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]] }

From 9019dc3bb14e7cb4d54738603eaa872c489b322d Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 11:31:35 +0200
Subject: [PATCH 21/23] Update .github/workflows/branch.yml

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 431dae2e52..5d12758d1c 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,4 +13,4 @@ jobs:
       - uses: actions/checkout@v1
       - name: Check PRs
         run: |
-         [[ ${GITHUB_HEAD_REF} = "patch" ]] || { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]] }
+         [[ ${GITHUB_HEAD_REF} = "patch" ]] || { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_BASE_REF} = "master" ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; }

From 6e7262faee3db3b937c5881fc1518dbdedaea037 Mon Sep 17 00:00:00 2001
From: Maxime Garcia <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 11:38:27 +0200
Subject: [PATCH 22/23] Update .github/workflows/branch.yml

---
 .github/workflows/branch.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
index 5d12758d1c..741af20632 100644
--- a/.github/workflows/branch.yml
+++ b/.github/workflows/branch.yml
@@ -13,4 +13,4 @@ jobs:
       - uses: actions/checkout@v1
       - name: Check PRs
         run: |
-         [[ ${GITHUB_HEAD_REF} = "patch" ]] || { [[ $(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* ]]

From 9893a3b6a945fa7b2c73405a83792a7dafb2ec7d Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Tue, 22 Oct 2019 12:17:09 +0200
Subject: [PATCH 23/23] fix travis branch protection

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index e08837e8fc..fdc9ffb066 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -9,7 +9,7 @@ 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