diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
index e32e0c2f68..b4a3147f40 100644
--- a/.github/ISSUE_TEMPLATE/bug_report.md
+++ b/.github/ISSUE_TEMPLATE/bug_report.md
@@ -31,5 +31,8 @@ A clear and concise description of what you expected to happen.
 **Container (please complete the following information):**
  - tag: [e.g. 1.0.0]
 
+**Sarek (please complete the following information):**
+ - version: [e.g. 2.1.0]
+
 **Additional context**
 Add any other context about the problem here.
diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
index 56ecb2d715..6721a7a797 100644
--- a/.github/RELEASE_CHECKLIST.md
+++ b/.github/RELEASE_CHECKLIST.md
@@ -1,24 +1,34 @@
 # Release checklist
-This checklist is for our own reference
-
-1. Check that everything is up to date and ready to go
-    - Travis tests are passing
-    - Manual tests on Bianca are passing
-2. Increase version numbers
-3. Update version numbers in code: `configuration/base.config`
-4. Build, and get the containers.
-    - `./scripts/do_all.sh --push --tag <VERSION>`
-    - `./scripts/do_all.sh --pull --tag <VERSION>`
-5. Test against sample data.
-    - Check for any command line errors
-    - Check version numbers are printed correctly
-    - `./scripts/test.sh -p docker --tag <VERSION>`
-    - `./scripts/test.sh -p singularity --tag <VERSION>`
-    - `./scripts/test.sh -p singularityPath --tag <VERSION>`
-6. Commit and push version updates
-7. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub
-8. Choose an appropriate codename for the release
-9. Update [bio.tools](https://bio.tools/Sarek) with the new release
-10. Tweet that new version is released
-11. Commit and push. Continue making more awesome :metal:
-12. Have fika :cake:
+
+> This checklist is for our own reference, to help us prepare a new release
+
+1.  Check that everything is ready to go
+
+    -   [PRs](https://github.com/SciLifeLab/Sarek/pulls) are merged
+    -   [Travis tests](https://travis-ci.org/SciLifeLab/Sarek/branches) are passing on `dev`
+
+2.  Increase version number following [semantic versioning](http://semver.org/spec/v2.0.0.html)
+3.  Choose an appropriate codename for the release
+    -   i.e. Peaks in [Sarek National Park](https://en.wikipedia.org/wiki/Sarek_National_Park#Topography)
+4.  Build docker containers.
+
+    -   `./scripts/do_all.sh --tag <VERSION>`
+
+5.  Test against sample data.
+
+    -   `./scripts/test.sh -p docker --tag <VERSION>`
+    -   Check for any command line errors
+
+6.  Use script to update version in files:
+
+    -   `./scripts/do_release.sh -r "<VERSION>" -c "<CODENAME>"`
+
+7.  Push latest updates
+8.  Make a PR against `dev`
+9.  Merge said PR
+10. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub
+11. Update [bio.tools](https://bio.tools/Sarek) with the new release details
+12. Tweet that a new version is released
+13. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
+14. Commit and push. Continue making more awesome :metal:
+15. Have fika :cake:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 93585f8f9e..50c2eeb05a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,225 +1,258 @@
 # Changelog
+
 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]
+
 ### `Added`
-- [#613](https://github.com/SciLifeLab/Sarek/pull/613) - Add Issue Templates (bug report and feature request)
-- [#614](https://github.com/SciLifeLab/Sarek/pull/614) - Add PR Template
-- [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Add presentation
-- [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Update documentation
-- [#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
+
+-   [#613](https://github.com/SciLifeLab/Sarek/pull/613) - Add Issue Templates (bug report and feature request)
+-   [#614](https://github.com/SciLifeLab/Sarek/pull/614) - Add PR Template
+-   [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Add presentation
+-   [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Update documentation
+-   [#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
 
 ### `Changed`
-- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
-- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
-- [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines`
-- [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Improve install script
-- [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Simplify tests
-- [#627](https://github.com/SciLifeLab/Sarek/pull/627), [#629](https://github.com/SciLifeLab/Sarek/pull/629), [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Refactor docs
-- [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Refactor config
-- [#632](https://github.com/SciLifeLab/Sarek/pull/632) - Use 2 threads and 2 cpus FastQC processes
-- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Update tool version gathering
-- [#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
+
+-   [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
+-   [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
+-   [#615](https://github.com/SciLifeLab/Sarek/pull/615) - Use `splitCsv` instead of `readlines`
+-   [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Improve install script
+-   [#621](https://github.com/SciLifeLab/Sarek/pull/621), [#638](https://github.com/SciLifeLab/Sarek/pull/638) - Simplify tests
+-   [#627](https://github.com/SciLifeLab/Sarek/pull/627), [#629](https://github.com/SciLifeLab/Sarek/pull/629), [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Refactor docs
+-   [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Refactor config
+-   [#632](https://github.com/SciLifeLab/Sarek/pull/632) - Use 2 threads and 2 cpus FastQC processes
+-   [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Update tool version gathering
+-   [#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
 
 ### `Removed`
-- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template
-- [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Remove old Dockerfiles
-- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Remove old comments
+
+-   [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template
+-   [#629](https://github.com/SciLifeLab/Sarek/pull/629) - Remove old Dockerfiles
+-   [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Remove old comments
 
 ### `Fixed`
-- [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Fix VEP tests
-- [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Fix links in MD files
+
+-   [#621](https://github.com/SciLifeLab/Sarek/pull/621) - Fix VEP tests
+-   [#637](https://github.com/SciLifeLab/Sarek/pull/637) - Fix links in MD files
+
 ## [2.1.0] - Ruotes - 2018-08-14
 
 ### `Added`
-- [#555](https://github.com/SciLifeLab/Sarek/pull/555) - `snpEff` output into `VEP`
-- [#556](https://github.com/SciLifeLab/Sarek/pull/556) - `Strelka` Best Practices
-- [#563](https://github.com/SciLifeLab/Sarek/pull/563) - Use `SnpEFF` reports in `MultiQC`
-- [#568](https://github.com/SciLifeLab/Sarek/pull/568) - `VCFTools` process `RunVcftools` for QC
-- [#574](https://github.com/SciLifeLab/Sarek/pull/574), [#580](https://github.com/SciLifeLab/Sarek/pull/580) - Abstracts for NPMI, JOBIM and  EACR25
-- [#577](https://github.com/SciLifeLab/Sarek/pull/577) - New repository for testing: [Sarek-data](https://github.com/SciLifeLab/Sarek-data)
-- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New library `QC` for functions `bamQC`, `bcftools`, `samtoolsStats`, `vcftools`, `getVersionBCFtools`, `getVersionGATK`, `getVersionManta`, `getVersionSnpEFF`, `getVersionStrelka`, `getVersionVCFtools`, `getVersionVEP`
-- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New Processes `GetVersionBCFtools`, `GetVersionGATK`, `GetVersionManta`, `GetVersionSnpEFF`, `GetVersionStrelka`, `GetVersionVCFtools`, `GetVersionVEP`
-- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - new Python script `bin/scrape_tool_versions.py` inspired by @ewels and @apeltzer
-- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New QC Process `RunVcftools`
-- [#596](https://github.com/SciLifeLab/Sarek/pull/596) - New profile for BinAC cluster
-- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - New function `sarek_ascii()` in `SarekUtils`
-- [#599](https://github.com/SciLifeLab/Sarek/pull/599), [#602](https://github.com/SciLifeLab/Sarek/pull/602) - New Process `CompressVCF`
-- [#601](https://github.com/SciLifeLab/Sarek/pull/601), [#603](https://github.com/SciLifeLab/Sarek/pull/603) - Container for GATK4
-- [#606](https://github.com/SciLifeLab/Sarek/pull/606) - Add test data as a submodule from [`Sarek-data`](https://github.com/SciLifeLab/Sarek-data)
-- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Add documentation on how to install Nextflow on `bianca`
+
+-   [#555](https://github.com/SciLifeLab/Sarek/pull/555) - `snpEff` output into `VEP`
+-   [#556](https://github.com/SciLifeLab/Sarek/pull/556) - `Strelka` Best Practices
+-   [#563](https://github.com/SciLifeLab/Sarek/pull/563) - Use `SnpEFF` reports in `MultiQC`
+-   [#568](https://github.com/SciLifeLab/Sarek/pull/568) - `VCFTools` process `RunVcftools` for QC
+-   [#574](https://github.com/SciLifeLab/Sarek/pull/574), [#580](https://github.com/SciLifeLab/Sarek/pull/580) - Abstracts for NPMI, JOBIM and  EACR25
+-   [#577](https://github.com/SciLifeLab/Sarek/pull/577) - New repository for testing: [Sarek-data](https://github.com/SciLifeLab/Sarek-data)
+-   [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New library `QC` for functions `bamQC`, `bcftools`, `samtoolsStats`, `vcftools`, `getVersionBCFtools`, `getVersionGATK`, `getVersionManta`, `getVersionSnpEFF`, `getVersionStrelka`, `getVersionVCFtools`, `getVersionVEP`
+-   [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New Processes `GetVersionBCFtools`, `GetVersionGATK`, `GetVersionManta`, `GetVersionSnpEFF`, `GetVersionStrelka`, `GetVersionVCFtools`, `GetVersionVEP`
+-   [#595](https://github.com/SciLifeLab/Sarek/pull/595) - new Python script `bin/scrape_tool_versions.py` inspired by @ewels and @apeltzer
+-   [#595](https://github.com/SciLifeLab/Sarek/pull/595) - New QC Process `RunVcftools`
+-   [#596](https://github.com/SciLifeLab/Sarek/pull/596) - New profile for BinAC cluster
+-   [#597](https://github.com/SciLifeLab/Sarek/pull/597) - New function `sarek_ascii()` in `SarekUtils`
+-   [#599](https://github.com/SciLifeLab/Sarek/pull/599), [#602](https://github.com/SciLifeLab/Sarek/pull/602) - New Process `CompressVCF`
+-   [#601](https://github.com/SciLifeLab/Sarek/pull/601), [#603](https://github.com/SciLifeLab/Sarek/pull/603) - Container for GATK4
+-   [#606](https://github.com/SciLifeLab/Sarek/pull/606) - Add test data as a submodule from [`Sarek-data`](https://github.com/SciLifeLab/Sarek-data)
+-   [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Add documentation on how to install Nextflow on `bianca`
 
 ### `Changed`
-- [#557](https://github.com/SciLifeLab/Sarek/pull/557), [#583](https://github.com/SciLifeLab/Sarek/pull/583), [#585](https://github.com/SciLifeLab/Sarek/pull/585), [#588](https://github.com/SciLifeLab/Sarek/pull/588) - Update help
-- [#560](https://github.com/SciLifeLab/Sarek/pull/560) - GitHub langage for the repository is now `Nextflow`
-- [#561](https://github.com/SciLifeLab/Sarek/pull/561) - `do_all.sh` build only containers for one genome reference (default `GRCh38`) only
-- [#571](https://github.com/SciLifeLab/Sarek/pull/571) - Only one container for all QC tools
-- [#582](https://github.com/SciLifeLab/Sarek/pull/582), [#587](https://github.com/SciLifeLab/Sarek/pull/587) - Update figures
-- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - Function `defineDirectoryMap()` is now part of `SarekUtils`
-- [#595](https://github.com/SciLifeLab/Sarek/pull/595) - Process `GenerateMultiQCconfig` replace by function `createMultiQCconfig()`
-- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Move `checkFileExtension()`, `checkParameterExistence()`, `checkParameterList()`, `checkReferenceMap()`, `checkRefExistence()`, `extractBams()`, `extractGenders()`, `returnFile()`, `returnStatus()` and `returnTSV()` functions to `SarekUtils`
-- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - `extractBams()` now takes an extra parameter.
-- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Replace depreciated operator `phase` by `join`.
-- [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Reduce data footprint for Process `CreateRecalibrationTable`
-- [#599](https://github.com/SciLifeLab/Sarek/pull/599) - Merge is tested with `ANNOTATEALL`
-- [#604](https://github.com/SciLifeLab/Sarek/pull/604) - Synching `GRCh38` `wgs_calling_regions` bedfiles
-- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to GATK4
-- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - One container approach
-- [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
-- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
-- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace depreciated $name syntax with withName
+
+-   [#557](https://github.com/SciLifeLab/Sarek/pull/557), [#583](https://github.com/SciLifeLab/Sarek/pull/583), [#585](https://github.com/SciLifeLab/Sarek/pull/585), [#588](https://github.com/SciLifeLab/Sarek/pull/588) - Update help
+-   [#560](https://github.com/SciLifeLab/Sarek/pull/560) - GitHub langage for the repository is now `Nextflow`
+-   [#561](https://github.com/SciLifeLab/Sarek/pull/561) - `do_all.sh` build only containers for one genome reference (default `GRCh38`) only
+-   [#571](https://github.com/SciLifeLab/Sarek/pull/571) - Only one container for all QC tools
+-   [#582](https://github.com/SciLifeLab/Sarek/pull/582), [#587](https://github.com/SciLifeLab/Sarek/pull/587) - Update figures
+-   [#595](https://github.com/SciLifeLab/Sarek/pull/595) - Function `defineDirectoryMap()` is now part of `SarekUtils`
+-   [#595](https://github.com/SciLifeLab/Sarek/pull/595) - Process `GenerateMultiQCconfig` replace by function `createMultiQCconfig()`
+-   [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Move `checkFileExtension()`, `checkParameterExistence()`, `checkParameterList()`, `checkReferenceMap()`, `checkRefExistence()`, `extractBams()`, `extractGenders()`, `returnFile()`, `returnStatus()` and `returnTSV()` functions to `SarekUtils`
+-   [#597](https://github.com/SciLifeLab/Sarek/pull/597) - `extractBams()` now takes an extra parameter.
+-   [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Replace depreciated operator `phase` by `join`.
+-   [#597](https://github.com/SciLifeLab/Sarek/pull/597) - Reduce data footprint for Process `CreateRecalibrationTable`
+-   [#599](https://github.com/SciLifeLab/Sarek/pull/599) - Merge is tested with `ANNOTATEALL`
+-   [#604](https://github.com/SciLifeLab/Sarek/pull/604) - Synching `GRCh38` `wgs_calling_regions` bedfiles
+-   [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to GATK4
+-   [#607](https://github.com/SciLifeLab/Sarek/pull/607) - One container approach
+-   [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update Nextflow required version
+-   [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update CHANGELOG
+-   [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace depreciated $name syntax with withName
 
 ### `Fixed`
-- [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath`
-- [#566](https://github.com/SciLifeLab/Sarek/pull/566) - `slurmDownload` profile
-- [#579](https://github.com/SciLifeLab/Sarek/pull/579), [#584](https://github.com/SciLifeLab/Sarek/pull/584) - `Manta` output reorganized after modification for `Strelka Best Practices` process
-- [#585](https://github.com/SciLifeLab/Sarek/pull/583) - Trace file is plain txt
-- [#590](https://github.com/SciLifeLab/Sarek/pull/590), [#593](https://github.com/SciLifeLab/Sarek/pull/593) - Fix Singularity installation in Travis CI testing
-- [#598](https://github.com/SciLifeLab/Sarek/pull/598), [#601](https://github.com/SciLifeLab/Sarek/pull/601) - Fixes for  Python script `selectROI.py` to work with CLC viewer
+
+-   [#560](https://github.com/SciLifeLab/Sarek/pull/560) - Display message for `repository` and `containerPath`
+-   [#566](https://github.com/SciLifeLab/Sarek/pull/566) - `slurmDownload` profile
+-   [#579](https://github.com/SciLifeLab/Sarek/pull/579), [#584](https://github.com/SciLifeLab/Sarek/pull/584) - `Manta` output reorganized after modification for `Strelka Best Practices` process
+-   [#585](https://github.com/SciLifeLab/Sarek/pull/583) - Trace file is plain txt
+-   [#590](https://github.com/SciLifeLab/Sarek/pull/590), [#593](https://github.com/SciLifeLab/Sarek/pull/593) - Fix Singularity installation in Travis CI testing
+-   [#598](https://github.com/SciLifeLab/Sarek/pull/598), [#601](https://github.com/SciLifeLab/Sarek/pull/601) - Fixes for  Python script `selectROI.py` to work with CLC viewer
 
 ### `Removed`
-- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Remove Mutect1
+
+-   [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Remove Mutect1
 
 ## [2.0.0] - 2018-03-23
+
 ### `Added`
-- basic wrapper script
-- Abstract, posters and figures
-- ROI selector and FreeBayes sanitizer scripts
-- New logo and icon for the project
-- check for existing tumor/normal channel
-- `SarekUtils` with `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` functions
-- some `runOptions` for `docker` (prevent some user right problem)
-- This `CHANGELOG`
+
+-   basic wrapper script
+-   Abstract, posters and figures
+-   ROI selector and FreeBayes sanitizer scripts
+-   New logo and icon for the project
+-   check for existing tumor/normal channel
+-   `SarekUtils` with `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` functions
+-   some `runOptions` for `docker` (prevent some user right problem)
+-   This `CHANGELOG`
 
 ### `Changed`
-- `CAW` is now `Sarek`
-- Dissect Workflow in 5 new scripts: `annotate.nf`, `main.nf`, `germlineVC.nf`, `runMultiQC.nf` and `somaticVC.nf`
-- `report.html`, `timeline.html` and `trace.html` are generated in `Reports/`
-- `--version` is now used to define the workflow version
-- most params are now defined in the base.config file instead of in the scripts
-- update RELEASE_CHECKLIST.md
-- `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` in script functions are now called within `SarekUtils`
-- `nf_required_version` is now `params.nfRequiredVersion`
-- in `buildReferences.nf` script, channels now begin by `ch_`, and files by `f_`
-- use `PublishDir mode: 'link'` instead of `copy`
-- `directoryMap` now contains `params.outDir`
-- [#539](https://github.com/SciLifeLab/Sarek/issues/539) - use Nextflow support of scratch
-- reordered Travis CI tests
-- update documentation
-- `MultiQC` version in container from v`1.4` to v`1.5`
-- `vepgrch37` container base image from `release_90.6` to `release_92`
-- `vepgrch38` container base image from `release_90.6` to `release_92`
-- `VEP` version in containers from v`90` to v`91`
-- `nucleotidesPerSecond` is now `params.nucleotidesPerSecond`
-- default `params.tag` is now `latest` instead of current version, so --tag needs to be specified with the right version to be sure of using the `containers` corresponding
+
+-   `CAW` is now `Sarek`
+-   Dissect Workflow in 5 new scripts: `annotate.nf`, `main.nf`, `germlineVC.nf`, `runMultiQC.nf` and `somaticVC.nf`
+-   `report.html`, `timeline.html` and `trace.html` are generated in `Reports/`
+-   `--version` is now used to define the workflow version
+-   most params are now defined in the base.config file instead of in the scripts
+-   update RELEASE_CHECKLIST.md
+-   `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` in script functions are now called within `SarekUtils`
+-   `nf_required_version` is now `params.nfRequiredVersion`
+-   in `buildReferences.nf` script, channels now begin by `ch_`, and files by `f_`
+-   use `PublishDir mode: 'link'` instead of `copy`
+-   `directoryMap` now contains `params.outDir`
+-   [#539](https://github.com/SciLifeLab/Sarek/issues/539) - use Nextflow support of scratch
+-   reordered Travis CI tests
+-   update documentation
+-   `MultiQC` version in container from v`1.4` to v`1.5`
+-   `vepgrch37` container base image from `release_90.6` to `release_92`
+-   `vepgrch38` container base image from `release_90.6` to `release_92`
+-   `VEP` version in containers from v`90` to v`91`
+-   `nucleotidesPerSecond` is now `params.nucleotidesPerSecond`
+-   default `params.tag` is now `latest` instead of current version, so --tag needs to be specified with the right version to be sure of using the `containers` corresponding
 
 ### `Deprecated`
-- `standard` profile
-- `uppmax-localhost.config` file
+
+-   `standard` profile
+-   `uppmax-localhost.config` file
 
 ### `Removed`
-- `scripts/skeleton_batch.sh`
-- old data and tsv files
-- UPPMAX directories from containers
-- `--step` in `annotate.nf`, `germlineVC.nf` and `somatic.nf`
-- some `runOptions` for Singularity (binding not needed anymore on UPPMAX)
-- `download` profile
+
+-   `scripts/skeleton_batch.sh`
+-   old data and tsv files
+-   UPPMAX directories from containers
+-   `--step` in `annotate.nf`, `germlineVC.nf` and `somatic.nf`
+-   some `runOptions` for Singularity (binding not needed anymore on UPPMAX)
+-   `download` profile
 
 ### `Fixed`
-- [#533](https://github.com/SciLifeLab/Sarek/issues/533) - Replace `VEP` `--pick` option by `--per_gene`
-- [#530](https://github.com/SciLifeLab/Sarek/issues/530) - use `$PWD` for default `outDir`
+
+-   [#533](https://github.com/SciLifeLab/Sarek/issues/533) - Replace `VEP` `--pick` option by `--per_gene`
+-   [#530](https://github.com/SciLifeLab/Sarek/issues/530) - use `$PWD` for default `outDir`
 
 ## [1.2.5] - 2018-01-18
 
 ### `Added`
-- Zenodo for DOI
-- Delivery README
-- Document use of the `--sampleDir` option
-- Contributing Guidelines
-- Issue Templates
-- Release Checklist
-- `--outDir`
-- `awsbatch` profile
-- `aws-batch.config` config file
-- `--noBAMQC` params (failing sometimes on Bianca)
+
+-   Zenodo for DOI
+-   Delivery README
+-   Document use of the `--sampleDir` option
+-   Contributing Guidelines
+-   Issue Templates
+-   Release Checklist
+-   `--outDir`
+-   `awsbatch` profile
+-   `aws-batch.config` config file
+-   `--noBAMQC` params (failing sometimes on Bianca)
 
 ### `Changed`
-- Update `Nextflow` to `0.26.0` (new fancy report + AWS Batch)
-- Extra time on Travis CI testing
-- Replace `bundleDir` by `params.genome_base`
-- Update `MultiQC` to `1.3` (MEGAQC FTW)
-- Move and rename some test files
+
+-   Update `Nextflow` to `0.26.0` (new fancy report + AWS Batch)
+-   Extra time on Travis CI testing
+-   Replace `bundleDir` by `params.genome_base`
+-   Update `MultiQC` to `1.3` (MEGAQC FTW)
+-   Move and rename some test files
 
 ### `Fixed`
-- Version of COSMIC GRCh37 v83
-- Write an error message when `--sampleDir` does not find any FASTQ files
-- `base.config` for ConcatVCF process
-- File specification for recalibrationReport in RecalibrateBam process (got error on AWS Batch)
+
+-   Version of COSMIC GRCh37 v83
+-   Write an error message when `--sampleDir` does not find any FASTQ files
+-   `base.config` for ConcatVCF process
+-   File specification for recalibrationReport in RecalibrateBam process (got error on AWS Batch)
 
 ## [1.2.4] - 2017-10-27
 
 ### `Fixed`
-- [#488](https://github.com/SciLifeLab/Sarek/issues/488) - Better CPU requirements for `ConcatVCF`
-- [#489](https://github.com/SciLifeLab/Sarek/issues/489) - Exception handling for `ASCAT`
-- [#490](https://github.com/SciLifeLab/Sarek/issues/490) - CPU requirements for `runSingleStrelka` and `runSingleManta`
+
+-   [#488](https://github.com/SciLifeLab/Sarek/issues/488) - Better CPU requirements for `ConcatVCF`
+-   [#489](https://github.com/SciLifeLab/Sarek/issues/489) - Exception handling for `ASCAT`
+-   [#490](https://github.com/SciLifeLab/Sarek/issues/490) - CPU requirements for `runSingleStrelka` and `runSingleManta`
 
 ## [1.2.3] - 2017-10-18
 
 ### `Fixed`
-- [#475](https://github.com/SciLifeLab/Sarek/issues/475) - 16 cpus for local executor
-- [#357](https://github.com/SciLifeLab/Sarek/issues/357) - `ASCAT` works for GRCh38
-- [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on `/scratch`
-- [#480](https://github.com/SciLifeLab/Sarek/issues/480) - No `tsv` file needed for step `annotate`
+
+-   [#475](https://github.com/SciLifeLab/Sarek/issues/475) - 16 cpus for local executor
+-   [#357](https://github.com/SciLifeLab/Sarek/issues/357) - `ASCAT` works for GRCh38
+-   [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on `/scratch`
+-   [#480](https://github.com/SciLifeLab/Sarek/issues/480) - No `tsv` file needed for step `annotate`
 
 ## [1.2.2] - 2017-10-06
 
 ### `Fixed`
-- [#479](https://github.com/SciLifeLab/Sarek/issues/479) - Typo in `uppmax-localhost.config`
+
+-   [#479](https://github.com/SciLifeLab/Sarek/issues/479) - Typo in `uppmax-localhost.config`
 
 ## [1.2.1] - 2017-10-06
 
 ### `Changed`
-- `runascat` and `runconvertallelecounts` containers are now replaced by `r-base`
-- `willmclaren/ensembl-vep:release_90.5` is now base for `vepgrch37` and `vepgrch38`
+
+-   `runascat` and `runconvertallelecounts` containers are now replaced by `r-base`
+-   `willmclaren/ensembl-vep:release_90.5` is now base for `vepgrch37` and `vepgrch38`
 
 ### `Removed`
-- `vep` container
-- `strelka_config.ini` file
+
+-   `vep` container
+-   `strelka_config.ini` file
 
 ### `Fixed`
-- [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on /scratch
-- [#472](https://github.com/SciLifeLab/Sarek/issues/472) - Update function to check Nextflow version
-- [#473](https://github.com/SciLifeLab/Sarek/issues/473) - Remove `returnMin()` function
+
+-   [#471](https://github.com/SciLifeLab/Sarek/issues/471) - Running `Singularity` on /scratch
+-   [#472](https://github.com/SciLifeLab/Sarek/issues/472) - Update function to check Nextflow version
+-   [#473](https://github.com/SciLifeLab/Sarek/issues/473) - Remove `returnMin()` function
 
 ## [1.2.0] - 2017-10-02
 
 ### `Changed`
-- Fix version for Manuscript
+
+-   Fix version for Manuscript
 
 ## [1.1] - 2017-09-15
 
 ### `Added`
-- Singularity possibilities
+
+-   Singularity possibilities
 
 ### `Changed`
-- Reports made by default
-- Intervals file can be a bed file
-- Normal sample preprocessing + HaplotypeCaller is possible
-- Better Travis CI tests
+
+-   Reports made by default
+-   Intervals file can be a bed file
+-   Normal sample preprocessing + HaplotypeCaller is possible
+-   Better Travis CI tests
 
 ### `Fixed`
-- Memory requirements
+
+-   Memory requirements
 
 ## [1.0] - 2017-02-16
 
 ### `Added`
-- Docker possibilities
+
+-   Docker possibilities
 
 ## [0.9] - 2016-11-16
 
diff --git a/Dockerfile b/Dockerfile
index 340e699e71..08425200ac 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,5 +6,5 @@ LABEL \
 	maintainer="Maxime Garcia <maxime.garcia@scilifelab.se>, Szilveszter Juhos <Szilveszter.Juhos@scilifelab.se>"
 
 COPY environment.yml /
-RUN conda env update -n root -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/bin:$PATH
+RUN conda env create -f /environment.yml && conda clean -a
+ENV PATH /opt/conda/envs/sarek-2.1.0/bin:$PATH
diff --git a/docs/RELEASE.md b/docs/RELEASE.md
new file mode 100644
index 0000000000..5b74da67ff
--- /dev/null
+++ b/docs/RELEASE.md
@@ -0,0 +1,38 @@
+# RELEASE
+
+> This document is for helping Sarek core developers and anyone joining the team to prepare a new release
+
+## [CHECKLIST](https://github.com/SciLifeLab/Sarek/blob/master/.github/RELEASE_CHECKLIST.md)
+
+This checklist is for our own reference, to help us prepare a new release.
+Just follow it and be sure to check every item on the list.
+
+## [Helper script](https://github.com/SciLifeLab/Sarek/blob/master/scripts/do_release.sh)
+
+This script will update the version number in the following files:
+
+-   [CHANGELOG.md](https://github.com/SciLifeLab/Sarek/blob/master/CHANGELOG.md)
+    -   Will change Unreleased to correct version number and add codename and date
+-   [Dockerfile](https://github.com/SciLifeLab/Sarek/blob/master/Dockerfile)
+    -   Will update to correct version number
+-   [Singularity](https://github.com/SciLifeLab/Sarek/blob/master/Singularity)
+    -   Will update to correct version number
+-   [conf/base.config](https://github.com/SciLifeLab/Sarek/blob/master/conf/base.config)
+    -   Will update to correct version number
+
+### Usage
+
+### Usage
+
+```bash
+./scripts/do_release.sh -r "<RELEASE>" -c "<CODENAME>"
+```
+
+-   `-r|--release` specify the new version number
+-   `-c|--codename` specify the codename
+
+### Example
+
+```bash
+./scripts/do_release.sh -r "2.2.0" -c "Skårki"
+```
diff --git a/scripts/do_release.sh b/scripts/do_release.sh
new file mode 100755
index 0000000000..88caf682a5
--- /dev/null
+++ b/scripts/do_release.sh
@@ -0,0 +1,43 @@
+#!/bin/bash
+set -xeuo pipefail
+
+CODENAME=''
+RELEASE=''
+
+while [[ $# -gt 0 ]]
+do
+  key=$1
+  case $key in
+    -c|--codename)
+    CODENAME=$2
+    shift # past argument
+    shift # past value
+    ;;
+    -r|--release)
+    RELEASE=$2
+    shift # past argument
+    shift # past value
+    ;;
+  esac
+done
+
+if [[ $CODENAME == "" ]]
+then
+  echo "No codename specified"
+  exit
+fi
+
+if [[ $RELEASE == "" ]]
+then
+  echo "No release specified"
+  exit
+fi
+
+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-$RELEASE/g" Singularity
+sed -i "s/version = '[0-9\.]\+'/version = '$RELEASE'/g" conf/base.config
+
+git commit CHANGELOG.md Dockerfile Singularity conf/base.config -m "preparing release $RELEASE [skip ci]"