Merge pull request #642 from MaxUlysse/conda

Update conda channel order priorities

CHANGELOG.md

@@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#620](https://github.com/SciLifeLab/Sarek/pull/620) - Add `tmp/` to `.gitignore`
 -   [#625](https://github.com/SciLifeLab/Sarek/pull/625) - Add [`pathfindr`](https://github.com/NBISweden/pathfindr) as a submodule
 -   [#639](https://github.com/SciLifeLab/Sarek/pull/639) - Add a complete example analysis to docs
--   [#640](https://github.com/SciLifeLab/Sarek/pull/640) - Add helper script for changing version number
+-   [#640](https://github.com/SciLifeLab/Sarek/pull/640), [#642](https://github.com/SciLifeLab/Sarek/pull/642) - Add helper script for changing version number
 
 ### `Changed`
 
@@ -32,6 +32,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Use correct `.simg` extension for Singularity images
 -   [#639](https://github.com/SciLifeLab/Sarek/pull/639) - Smaller refactoring of the docs
 -   [#640](https://github.com/SciLifeLab/Sarek/pull/640) - Update RELEASE_CHECKLIST
+-   [#642](https://github.com/SciLifeLab/Sarek/pull/642) - Update conda channel order priorities
+-   [#642](https://github.com/SciLifeLab/Sarek/pull/642) - MultiQC 1.5 -> 1.6
+-   [#642](https://github.com/SciLifeLab/Sarek/pull/642) - Qualimap 2.2.2a -> 2.2.2b
+-   [#642](https://github.com/SciLifeLab/Sarek/pull/642) - VCFanno 0.2.8 -> 0.3.0
+-   [#642](https://github.com/SciLifeLab/Sarek/pull/642) - VCFtools 0.1.15 -> 0.1.16
 
 ### `Removed`
 

docs/CONTAINERS.md

@@ -79,7 +79,7 @@ We provide script to build/push or pull all containers
 
 ### sarek [![sarek-docker status][sarek-docker-badge]][sarek-docker-link]
 
-- Based on `debian:8.9`
+- Based on `nfcore/base:latest`
 - Contain **[BCFTools][bcftools-link]** 1.8
 - Contain **[BWA][bwa-link]** 0.7.17
 - Contain **[FastQC][fastqc-link]** 0.11.7
@@ -88,12 +88,12 @@ We provide script to build/push or pull all containers
 - Contain **[HTSlib][htslib-link]** 1.9
 - Contain **[IGVtools][igvtools-link]** 2.3.93
 - Contain **[Manta][manta-link]** 1.4.0
-- Contain **[MultiQC][multiqc-link]** 1.5
-- Contain **[Qualimap][qualimap-link]** 2.2.2a
+- Contain **[MultiQC][multiqc-link]** 1.6
+- Contain **[Qualimap][qualimap-link]** 2.2.2b
 - Contain **[samtools][samtools-link]** 1.8
 - Contain **[Strelka2][strelka-link]** 2.9.3
-- Contain **[VCFanno][vcfanno-link]** 0.2.8
-- Contain **[VCFtools][vcftools-link]** 0.1.15
+- Contain **[VCFanno][vcfanno-link]** 0.3.0
+- Contain **[VCFtools][vcftools-link]** 0.1.16
 
 ### snpeff [![snpeff-docker status][snpeff-docker-badge]][snpeff-docker-link]
 

environment.yml

@@ -1,24 +1,23 @@
 # You can use this file to create a conda environment for this pipeline:
 # conda env create -f environment.yml
-name: sarek
+name: sarek-2.1.0
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 
 dependencies:
   - bcftools=1.8
   - bwa=0.7.17
-  - conda-forge::openjdk=8.0.144 # Needed for FastQC docker - see bioconda/bioconda-recipes#5026
   - fastqc=0.11.7
   - freebayes=1.2.0
   - gatk4=4.0.6.0
   - htslib=1.9
   - igvtools=2.3.93
   - manta=1.4.0
-  - multiqc=1.5
-  - qualimap=2.2.2a
+  - multiqc=1.6
+  - qualimap=2.2.2b
   - samtools=1.8
   - strelka=2.9.3
-  - vcfanno=0.2.8
-  - vcftools=0.1.15
+  - vcfanno=0.3.0
+  - vcftools=0.1.16

scripts/do_release.sh

@@ -37,7 +37,8 @@ echo "Preparing release $RELEASE - $CODENAME"
 
 sed -i "s/\[Unreleased\]/[$RELEASE] - $CODENAME - $(date +'%Y-%m-%d')/g" CHANGELOG.md
 sed -i "s/sarek-[0-9\.]\+/sarek-$RELEASE/g" Dockerfile
+sed -i "s/sarek-[0-9\.]\+/sarek-$RELEASE/g" environment.yml
 sed -i "s/sarek-[0-9\.]\+/sarek-$RELEASE/g" Singularity
 sed -i "s/version = '[0-9\.]\+'/version = '$RELEASE'/g" conf/base.config
 
-git commit CHANGELOG.md Dockerfile Singularity conf/base.config -m "preparing release $RELEASE [skip ci]"
+git commit CHANGELOG.md Dockerfile environment.yml Singularity conf/base.config -m "preparing release $RELEASE [skip ci]"