nf-core bump-version . 2.5.1

fix script name in docs fix markdownlint fix autoMounts in singularity profile, closes nf-core#48 build 2.5.1 version of annotation containers update CHANGELOG Typo Update .github/workflows/branch.yml Update .github/workflows/branch.yml Update README.md
maxulysse · May 18, 2020 · 2ff514b · 2ff514b
1 parent eeffa14
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,39 +6,42 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
+      SAREK_TAG: dev
     steps:
       - checkout
       - setup_remote_docker
       - run:
-          command: docker build -t nfcore/sareksnpeff:dev.${GENOME} containers/snpeff/. --build-arg GENOME=${GENOME} --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION}
+          command: docker build -t nfcore/sareksnpeff:${SAREK_TAG}.${GENOME} containers/snpeff/. --build-arg GENOME=${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}
+          command: echo "$DOCKERHUB_PASS" | docker login -u "$DOCKERHUB_USERNAME" --password-stdin ; docker push nfcore/sareksnpeff:${SAREK_TAG}.${GENOME}
 
   snpeffgrch38:
     << : *buildsnpeff
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
+      SAREK_TAG: dev
 
   vepgrch37: &buildvep
     docker:
@@ -47,42 +50,47 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
+      SAREK_TAG: dev
     steps:
       - 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:${SAREK_TAG}.${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:${SAREK_TAG}.${GENOME}
 
   vepgrch38:
     << : *buildvep
     environment:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
+      SAREK_TAG: dev
 
 workflows:
   version: 2

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,4 +13,4 @@ jobs:
       # PRs are only ok if coming from an nf-core `dev` branch or a fork `patch` branch
       - name: Check PRs
         run: |
-          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
+          { [[ $(git remote get-url origin) == *nf-core/sarek ]] && [[ ${GITHUB_HEAD_REF} = "dev" ]]; } || [[ ${GITHUB_HEAD_REF} == "patch" ]]
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -192,6 +192,16 @@ Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.
 - [#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.
 
+## [2.5.1] - 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
 
 Ålkatj is one of the main massif in the Sarek National Park.

diff --git a/README.md b/README.md
@@ -130,26 +130,12 @@ For further information or help, don't hesitate to get in touch on [Slack](https
 
 ## Citation
 
-<<<<<<< HEAD
 If you use `nf-core/sarek` for your analysis, please cite the `Sarek` article as follows:
 > Garcia M, Juhos S, Larsson M et al. **Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants [version 1; peer review: 2 approved]** *F1000Research* 2020, 9:63 [doi: 10.12688/f1000research.16665.1](https://f1000research.com/articles/9-63/v1).
 
 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` publication as follows:
-=======
-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)
-<<<<<<< HEAD
-<<<<<<< HEAD
->>>>>>> 8518d36... added script to help downstream analysis, adding RankScore for Scout
-=======
->>>>>>> 6aa1091... fix markdownlint
-=======
->>>>>>> 8518d36... added script to help downstream analysis, adding RankScore for Scout
->>>>>>> cb13187... added script to help downstream analysis, adding RankScore for Scout
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >

diff --git a/nextflow.config b/nextflow.config
@@ -198,8 +198,13 @@ manifest {
   homePage = 'https://github.com/nf-core/sarek'
   description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
   mainScript = 'main.nf'
+<<<<<<< HEAD
   nextflowVersion = '>=19.10.0'
   version = '2.6dev'
+=======
+  nextflowVersion = '>=19.04.0'
+  version = '2.5.1'
+>>>>>>> 8148546... nf-core bump-version . 2.5.1
 }
 
 // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over