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Merge pull request nf-core#552 from MaxUlysse/1.3.0
More fixes and enhancements for 2.0.0
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‎.github/RELEASE_CHECKLIST.md‎

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This checklist is for our own reference
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1. Check that everything is up to date and ready to go
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- Travis test is passing
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- Manual testing on Bianca is passing
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2. Increase version numbers.
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3. Update version numbers in code: `main.nf`, `buildContainers.nf`, `buildReferences.nf`
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4. If any changes on any containers, match the tag to current version `docker.config`, `singularity.config`, `singularity-path.config`.
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5. Build, and get the containers.
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- `./scripts/do_all.sh --push`
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- `./scripts/do_all.sh --pull`
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6. Test against sample data.
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3. Update version numbers in code: `configuration/base.config`
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4. Build, and get the containers.
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- `./scripts/do_all.sh --push --tag <VERSION>`
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- `./scripts/do_all.sh --pull --tag <VERSION>`
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5. Test against sample data.
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- Check for any command line errors
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- Check version numbers are printed correctly
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- `./scripts/test.sh -p docker`
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- `./scripts/test.sh -p singularity`
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- `./scripts/test.sh -p singularityPath`
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7. Commit and push version updates
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8. Make a [release](https://github.com/SciLifeLab/CAW/releases) on GitHub - list PRs as changelog.
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9. Tweet that new version is released
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10. Commit and push. Continue making more awesome :metal:
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11. Have fika :cake:
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- `./scripts/test.sh -p docker --tag <VERSION>`
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- `./scripts/test.sh -p singularity --tag <VERSION>`
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- `./scripts/test.sh -p singularityPath --tag <VERSION>`
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6. Commit and push version updates
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7. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub
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8. Tweet that new version is released
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9. Commit and push. Continue making more awesome :metal:
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10. Have fika :cake:

‎.travis.yml‎

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- docker
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env:
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=DIR TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=TOOLS TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=TOOLS TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=MANTA TOOL_INSTALL=all
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=DIR TOOL_INSTALL=all
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- NXF_VER=0.27.0 PROFILE=docker TEST=MANTA TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow
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- NXF_VER=0.27.0 PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow
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install: # Install Nextflow (and Singularity if needed)
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- "./scripts/install.sh --tool $TOOL_INSTALL"

‎CHANGELOG.md‎

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# Changelog
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All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
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and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
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## [Unreleased]
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- Python wrapper script
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## [2.0.0] - 2018-03-23
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### `Added`
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- basic wrapper script
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- Abstract, posters and figures
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- ROI selector and FreeBayes sanitizer scripts
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- New logo and icon for the project
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- check for existing tumor/normal channel
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- `lib/SarekUtils.groovy` with `checkParams`, `checkParameterList`, `checkParameterExistence` and `isAllowedParams` functions
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- some `runOptions` for `docker` (prevent some user right problem)
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- This `CHANGELOG`
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### `Changed`
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- `CAW` is now `Sarek`
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- Dissect Workflow in 5 new scripts: `annotate.nf`, `main.nf`, `germlineVC.nf`, `runMultiQC.nf` and `somaticVC.nf`
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- `report.html`, `timeline.html` and `trace.html` are generated in `Reports/`
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- `--version` is now used to define the workflow version
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- most params are now defined in the base.config file instead of in the scripts
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- update RELEASE_CHECKLIST.md
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- `checkParams`, `checkParameterList`, `checkParameterExistence` and `isAllowedParams` in script functions are now called within `SarekUtils`
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- `nf_required_version` is now `params.nfRequiredVersion`
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- in `buildReferences.nf` script, channels now begin by `ch_`, and files by `f_`
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- use `PublishDir mode: 'link'`` instead of `copy`
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- `directoryMap` now contains `params.outDir`
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- use Nextflow support of scratch (close #539)
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- reordered Travis CI tests
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- update documentation
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- `MultiQC` version in container from v`1.4` to v`1.5`
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- `vepgrch37` container base image from `release_90.6` to `release_92`
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- `vepgrch38` container base image from `release_90.6` to `release_92`
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- `VEP` version in containers from v`90` to v`91`
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- `nucleotidesPerSecond` is now `params.nucleotidesPerSecond`
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- 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
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### `Deprecated`
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- `standard` profile
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- `uppmax-localhost.config` file
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### `Removed`
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- `scripts/skeleton_batch.sh`
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- old data and tsv files
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- UPPMAX directories from containers
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- `--step` in `annotate.nf`, `germlineVC.nf` and `somatic.nf`
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- some `runOptions` for Singularity (binding not needed anymore on UPPMAX)
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- `download` profile
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### `Fixed`
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- Replace `VEP` `--pick` option by `--per_gene` (fix #533)
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- use `$PWD` for default `outDir` (fix #530)
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## [1.2.5] - 2018-01-18
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### `Added`
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- Zenodo for DOI
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- Delivery README
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- Document use of the `--sampleDir` option
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- Contributing Guidelines
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- Issue Templates
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- Release Checklist
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- `--outDir`
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- `awsbatch` profile
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- `aws-batch.config` config file
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- `--noBAMQC` params (failing sometimes on Bianca)
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### `Changed`
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- Update `Nextflow` to `0.26.0` (new fancy report + AWS Batch)
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- Extra time on Travis CI testing
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- Replace `bundleDir` by `params.genome_base`
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- Update `MultiQC` to `1.3` (MEGAQC FTW)
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- Move and rename some test files
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### `Fixed`
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- Version of COSMIC GRCh37 v83
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- Write an error message when `--sampleDir` does not find any FASTQ files
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- `base.config` for ConcatVCF process
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- File specification for recalibrationReport in RecalibrateBam process (got error on AWS Batch)
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## [1.2.4] - 2017-10-27
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### `Fixed`
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- Better CPU requirements for `ConcatVCF` (fix #488)
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- Exception handling for `ASCAT` (close #489)
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- CPU requirements for `runSingleStrelka` and `runSingleManta` (fix #490)
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## [1.2.3] - 2017-10-18
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### `Fixed`
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- 16 cpus for local executor (fix #475)
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- `ASCAT` works for GRCh38 (fix #357)
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- Running `Singularity` on /scratch (fix #471)
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- No tsv for step `annotate` (fix #480)
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## [1.2.2] - 2017-10-06
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### `Fixed`
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- Typo in `uppmax-localhost.config` (fix #479)
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## [1.2.1] - 2017-10-06
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### `Changed`
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- `runascat` and `runconvertallelecounts` containers are now replaced by `r-base`
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- `willmclaren/ensembl-vep:release_90.5` is now base for `vepgrch37` and `vepgrch38`
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### `Removed`
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- `vep` container
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- `strelka_config.ini` file
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### `Fixed`
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- Running `Singularity` on /scratch (fix #471)
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- Update function to check Nextflow version (fix #472)
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- Remove `returnMin()` function (fix #473)
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## [1.2.0] - 2017-10-02
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### `Changed`
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- Fix version for Manuscript
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## [1.1] - 2017-09-15
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### `Added`
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- Singularity possibilities
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### `Changed`
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- Reports made by default
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- Intervals file can be a bed file
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- Normal sample preprocessing + HaplotypeCaller is possible
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- Better Travis CI tests
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### `Fixed`
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- Memory requirements
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## [1.0] - 2017-02-16
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### `Added`
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- Docker possibilities
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## [0.9] - 2016-11-16
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## [0.8] - 2016-11-16
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## [0.1] - 2016-04-05

‎README.md‎

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## Contributions & Support
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If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
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If you would like to contribute to this pipeline, please see the [contributing guidelines](https://github.com/SciLifeLab/Sarek/blob/master/.github/CONTRIBUTING.md).
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For further information or help, don't hesitate to get in touch on [Gitter][gitter-link] or contact us: maxime.garcia@scilifelab.se, szilveszter.juhos@scilifelab.se
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## CHANGELOG
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- [CHANGELOG](https://github.com/SciLifeLab/Sarek/blob/master/CHANGELOG.md)
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## Authors
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* [Sebastian DiLorenzo](https://github.com/Sebastian-D)

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