✏️ added sort chr blocks to concatenateVCFs.sh

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
     environment:
       GENOME: GRCh37
       SNPEFF_CACHE_VERSION: "75"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
     steps:
       - checkout
       - setup_remote_docker
@@ -20,28 +20,28 @@ jobs:
     environment:
       GENOME: GRCh38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   snpeffgrcm38:
     << : *buildsnpeff
     environment:
       GENOME: GRCm38
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   snpeffcanfam3_1:
     << : *buildsnpeff
     environment:
       GENOME: CanFam3.1
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   snpeffwbcel235:
     << : *buildsnpeff
     environment:
       GENOME: WBcel235
       SNPEFF_CACHE_VERSION: "86"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   vepgrch37: &buildvep
     docker:
@@ -50,7 +50,7 @@ jobs:
       GENOME: GRCh37
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
     steps:
       - checkout
       - setup_remote_docker
@@ -67,31 +67,31 @@ jobs:
       GENOME: GRCh38
       SPECIES: homo_sapiens
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   vepgrcm38:
     << : *buildvep
     environment:
       GENOME: GRCm38
       SPECIES: mus_musculus
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   vepcanfam3_1:
     << : *buildvep
     environment:
       GENOME: CanFam3.1
       SPECIES: canis_familiaris
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
   vepwbcel235:
     << : *buildvep
     environment:
       GENOME: WBcel235
       SPECIES: caenorhabditis_elegans
       VEP_VERSION: "99"
-      SAREK_TAG: dev
+      SAREK_TAG: 2.7.1
 
 workflows:
   version: 2

.github/workflows/ci.yml

@@ -36,13 +36,13 @@ jobs:
             environment.yml
       - name: Build new docker image
         if: env.MATCHED_FILES
-        run: docker build --no-cache . -t nfcore/sarek:dev
+        run: docker build --no-cache . -t nfcore/sarek:2.7.1
 
       - name: Pull docker image
         if: ${{ !env.MATCHED_FILES }}
         run: |
           docker pull nfcore/sarek:dev
-          docker tag nfcore/sarek:dev nfcore/sarek:dev
+          docker tag nfcore/sarek:dev nfcore/sarek:2.7.1
 
       - name: Install Nextflow
         env:
@@ -74,8 +74,8 @@ jobs:
           NXF_VER: '20.04.0'
       - name: Pull docker image
         run: |
-          docker pull nfcore/sarek:dev
-          docker pull nfcore/sarek${{ matrix.tools }}:dev.${{ matrix.species }}
+          docker pull nfcore/sarek:2.7.1
+          docker pull nfcore/sarek${{ matrix.tools }}:2.7.1.${{ matrix.species }}
       - name: Run annotation test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test_annotation,docker --tools ${{ matrix.tools }}
 
@@ -96,7 +96,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.7.1
       - name: Get test data
         run: git clone --single-branch --branch sarek https://github.com/nf-core/test-datasets.git data
       - name: Run germline test
@@ -124,7 +124,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run test for minimal genomes
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --skip_qc all --genome ${{ matrix.genome }} ${{ matrix.intervals }} --tools Manta,mpileup,Strelka,FreeBayes
 
@@ -145,7 +145,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker
 
@@ -166,7 +166,7 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run ${{ matrix.profile }} test
         run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{ matrix.aligner }}
 
@@ -197,6 +197,6 @@ jobs:
           # Only check Nextflow pipeline minimum version
           NXF_VER: '20.04.0'
       - name: Pull docker image
-        run: docker pull nfcore/sarek:dev
+        run: docker pull nfcore/sarek:2.7.1
       - name: Run ${{ matrix.tool }} test
-        run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}
+        run: nextflow run ${GITHUB_WORKSPACE} -profile test_tool,docker --tools ${{ matrix.tool }} ${{ matrix.intervals }}

CHANGELOG.md

@@ -5,7 +5,9 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [dev](https://github.com/nf-core/sarek/tree/dev)
+## [2.7.1](https://github.com/nf-core/sarek/releases/tag/2.7.1) - Pårtejekna
+
+Pårtejekna is one of glaciers of the Pårte Massif.
 
 ### Added
 

Dockerfile

@@ -7,7 +7,7 @@ COPY environment.yml /
 RUN conda env create --quiet -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-sarek-3.0dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-2.7.1/bin:$PATH
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-sarek-3.0dev > nf-core-sarek-3.0dev.yml
+RUN conda env export --name nf-core-sarek-2.7.1 > nf-core-sarek-2.7.1.yml

bin/concatenateVCFs.sh

@@ -85,13 +85,19 @@ then
 	      tail -n +$((L+1)) ${vcf}
 	    done
 	  done
-	) | bgzip -@${cpus} > rawcalls.vcf.gz
+	) | bgzip -@${cpus} > rawcalls_tmp.vcf.gz
+	bgzip -d rawcalls_tmp.vcf.gz
+	bcftools sort rawcalls_tmp.vcf -o rawcalls.vcf
+	bgzip -@${cpus} rawcalls.vcf
 	tabix rawcalls.vcf.gz
+	rm rawcalls_tmp.vcf*
 else
         VCF=$(ls no_intervals*.vcf)
-        cp $VCF rawcalls.vcf 
+        cp $VCF rawcalls_tmp.vcf
+	bcftools sort rawcalls_tmp.vcf -o rawcalls.vcf
         bgzip -@${cpus} rawcalls.vcf
         tabix rawcalls.vcf.gz
+	rm rawcalls_tmp.vcf*
 fi
 
 set +u

conf/base.config

@@ -90,11 +90,11 @@ process {
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withName:Snpeff {
-    container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"}
+    container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:2.7.1' : "nfcore/sareksnpeff:2.7.1.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withLabel:VEP {
-    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:dev' : "nfcore/sarekvep:dev.${params.genome}"}
+    container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:2.7.1' : "nfcore/sarekvep:2.7.1.${params.genome}"}
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
   }
   withLabel:msisensor {

conf/test.config

@@ -33,11 +33,11 @@ params {
 
 process {
   withName:Snpeff {
-    container = 'nfcore/sareksnpeff:dev.WBcel235'
+    container = 'nfcore/sareksnpeff:2.7.1.WBcel235'
     maxForks = 1
   }
   withLabel:VEP {
-    container = 'nfcore/sarekvep:dev.WBcel235'
+    container = 'nfcore/sarekvep:2.7.1.WBcel235'
     maxForks = 1
   }
 }

containers/snpeff/Dockerfile

@@ -9,7 +9,7 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-sarek-snpeff-dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-snpeff-2.7.1/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
@@ -19,4 +19,4 @@ ARG SNPEFF_CACHE_VERSION=86
 RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION}
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-sarek-snpeff-dev > nf-core-sarek-snpeff-dev.yml
+RUN conda env export --name nf-core-sarek-snpeff-2.7.1 > nf-core-sarek-snpeff-2.7.1.yml

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: nf-core-sarek-snpeff-dev
+name: nf-core-sarek-snpeff-2.7.1
 channels:
   - conda-forge
   - bioconda

containers/vep/Dockerfile

@@ -9,7 +9,7 @@ COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
 
 # Add conda installation dir to PATH (instead of doing 'conda activate')
-ENV PATH /opt/conda/envs/nf-core-sarek-vep-dev/bin:$PATH
+ENV PATH /opt/conda/envs/nf-core-sarek-vep-2.7.1/bin:$PATH
 
 # Setup default ARG variables
 ARG GENOME=GRCh38
@@ -27,4 +27,4 @@ RUN vep_install \
   --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE
 
 # Dump the details of the installed packages to a file for posterity
-RUN conda env export --name nf-core-sarek-vep-dev > nf-core-sarek-vep-dev.yml
+RUN conda env export --name nf-core-sarek-vep-2.7.1 > nf-core-sarek-vep-2.7.1.yml

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: nf-core-sarek-vep-dev
+name: nf-core-sarek-vep-2.7.1
 channels:
   - conda-forge
   - bioconda

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-3.0dev
+name: nf-core-sarek-2.7.1
 channels:
   - conda-forge
   - bioconda
@@ -38,4 +38,4 @@ dependencies:
   - bioconda::vcfanno=0.3.2=0
   - bioconda::vcftools=0.1.16=he513fc3_4
   - conda-forge::pigz=2.3.4=hed695b0_1
-  - conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1
+  - conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1

nextflow.config

@@ -115,7 +115,7 @@ params {
 // Container slug
 // Stable releases should specify release tag (ie: `2.5.2`)
 // Developmental code should specify dev
-process.container = 'nfcore/sarek:dev'
+process.container = 'nfcore/sarek:2.7.1'
 
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
@@ -246,7 +246,7 @@ manifest {
   description = 'An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.04.0'
-  version = '3.0dev'
+  version = '2.7.1'
 }
 
 // Return the minimum between requirements and a maximum limit to ensure that resource requirements don't go over
@@ -263,4 +263,4 @@ def check_resource(obj) {
     } catch (all) {
         println "   ### ERROR ###   Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}'  is not valid! Using default value: $obj"
     }
-}
+}