more complete CHANGELOG

CHANGELOG.md

@@ -52,7 +52,98 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - some `runOptions` for Singularity (binding not needed anymore on UPPMAX)
 - `download` profile
 
-
 ### `Fixed`
 - Replace `VEP` `--pick` option by `--per_gene` (fix #533)
 - use `$PWD` for default `outDir` (fix #530)
+
+## [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)
+
+### `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
+
+### `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)
+
+## [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)
+
+## [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)
+
+## [1.2.2] - 2017-10-06
+
+### `Fixed`
+ - Typo in `uppmax-localhost.config` (fix #479)
+
+## [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`
+
+### `Removed`
+- `vep` container
+- `strelka_config.ini` file
+
+### `Fixed`
+- Running `Singularity` on /scratch (fix #471)
+- Update function to check Nextflow version (fix #472)
+- Remove `returnMin()` function (fix #473)
+
+## [1.2.0] - 2017-10-02
+
+### `Changed`
+- Fix version for Manuscript
+
+## [1.1] - 2017-09-15
+
+### `Added`
+- Singularity possibilities
+
+### `Changed`
+- Reports made by default
+- Intervals file can be a bed file
+- Normal sample preprocessing + HaplotypeCaller is possible
+- Better Travis CI tests
+
+### `Fixed`
+- Memory requirements
+
+## [1.0] - 2017-02-16
+
+### `Added`
+- Docker possibilities
+
+## [0.9] - 2016-11-16
+
+## [0.8] - 2016-11-16
+
+## [0.1] - 2016-04-05