More fixes and enhancements for 2.0.0

.github/RELEASE_CHECKLIST.md

@@ -2,20 +2,21 @@
 This checklist is for our own reference
 
 1. Check that everything is up to date and ready to go
+  - Travis test is passing
+  - Manual testing on Bianca is passing
 2. Increase version numbers.
-3. Update version numbers in code: `main.nf`, `buildContainers.nf`, `buildReferences.nf`
-4. If any changes on any containers, match the tag to current version `docker.config`, `singularity.config`, `singularity-path.config`.
-5. Build, and get the containers.
-  - `./scripts/do_all.sh --push`
-  - `./scripts/do_all.sh --pull`
-6. Test against sample data.
+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`
-  - `./scripts/test.sh -p singularity`
-  - `./scripts/test.sh -p singularityPath`
-7. Commit and push version updates
-8. Make a [release](https://github.com/SciLifeLab/CAW/releases) on GitHub - list PRs as changelog.
-9. Tweet that new version is released
-10. Commit and push. Continue making more awesome :metal:
-11. Have fika :cake:
+  - `./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. Tweet that new version is released
+9. Commit and push. Continue making more awesome :metal:
+10. Have fika :cake:

.travis.yml

@@ -8,19 +8,19 @@ services:
   - docker
 
 env:
-  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=DIR TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow
-  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow
-  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
-  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
-  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all
-  - NXF_VER=0.27.0 PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=TOOLS TOOL_INSTALL=all
   - NXF_VER=0.27.0 PROFILE=docker TEST=TOOLS TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=STEP TOOL_INSTALL=all
   - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=MANTA TOOL_INSTALL=all
+  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=ANNOTATESNPEFF TOOL_INSTALL=all
+  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=GERMLINE TOOL_INSTALL=all
+  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATEVEP TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=ANNOTATESNPEFF TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 SGT_VER=2.4.2 PROFILE=singularity TEST=DIR TOOL_INSTALL=all
   - NXF_VER=0.27.0 PROFILE=docker TEST=MANTA TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=STEP TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=GERMLINE TOOL_INSTALL=nextflow
+  - NXF_VER=0.27.0 PROFILE=docker TEST=DIR TOOL_INSTALL=nextflow
 
 install: # Install Nextflow (and Singularity if needed)
   - "./scripts/install.sh --tool $TOOL_INSTALL"

CHANGELOG.md

@@ -0,0 +1,149 @@
+# 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]
+- Python wrapper script
+
+## [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
+- `lib/SarekUtils.groovy` 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`
+- use Nextflow support of scratch (close #539)
+- 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
+
+### `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
+
+### `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

README.md

@@ -78,10 +78,14 @@ The Sarek pipeline comes with documentation in the `doc/` directory:
 
 ## Contributions & Support
 
-If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+If you would like to contribute to this pipeline, please see the [contributing guidelines](https://github.com/SciLifeLab/Sarek/blob/master/.github/CONTRIBUTING.md).
 
 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
 
+## CHANGELOG
+
+- [CHANGELOG](https://github.com/SciLifeLab/Sarek/blob/master/CHANGELOG.md)
+
 ## Authors
 
 * [Sebastian DiLorenzo](https://github.com/Sebastian-D)