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Changelog #616

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43 changes: 0 additions & 43 deletions .github/ISSUE_TEMPLATE.md
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88 changes: 70 additions & 18 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,59 @@ 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]
- Python wrapper script

## [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`
- [#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

### `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

### `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

### `Removed`
- [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Remove Mutect1
- [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Remove old Issue Template

## [2.0.0] - 2018-03-23
### `Added`
Expand All @@ -14,7 +66,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- ROI selector and FreeBayes sanitizer scripts
- New logo and icon for the project
- check for existing tumor/normal channel
- `lib/SarekUtils.groovy` with `checkParams`, `checkParameterList`, `checkParameterExistence` and `isAllowedParams` functions
- `SarekUtils` with `checkParams()`, `checkParameterList()`, `checkParameterExistence()` and `isAllowedParams()` functions
- some `runOptions` for `docker` (prevent some user right problem)
- This `CHANGELOG`

Expand All @@ -25,12 +77,12 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `--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`
- `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`
- use `PublishDir mode: 'link'` instead of `copy`
- `directoryMap` now contains `params.outDir`
- use Nextflow support of scratch (close #539)
- [#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`
Expand All @@ -53,8 +105,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `download` profile

### `Fixed`
- Replace `VEP` `--pick` option by `--per_gene` (fix #533)
- use `$PWD` for default `outDir` (fix #530)
- [#533](https://github.com/SciLifeLab/Sarek/issues/533) - Replace `VEP` `--pick` option by `--per_gene`
- [#530](https://github.com/SciLifeLab/Sarek/issues/530) - use `$PWD` for default `outDir`

## [1.2.5] - 2018-01-18

Expand Down Expand Up @@ -86,22 +138,22 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [1.2.4] - 2017-10-27

### `Fixed`
- Better CPU requirements for `ConcatVCF` (fix #488)
- Exception handling for `ASCAT` (close #489)
- CPU requirements for `runSingleStrelka` and `runSingleManta` (fix #490)
- [#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`
- 16 cpus for local executor (fix #475)
- `ASCAT` works for GRCh38 (fix #357)
- Running `Singularity` on /scratch (fix #471)
- No tsv for step `annotate` (fix #480)
- [#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`
- Typo in `uppmax-localhost.config` (fix #479)
- [#479](https://github.com/SciLifeLab/Sarek/issues/479) - Typo in `uppmax-localhost.config`

## [1.2.1] - 2017-10-06

Expand All @@ -114,9 +166,9 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
- `strelka_config.ini` file

### `Fixed`
- Running `Singularity` on /scratch (fix #471)
- Update function to check Nextflow version (fix #472)
- Remove `returnMin()` function (fix #473)
- [#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

Expand Down