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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[2.3.FIX1] - 2019-03-04

Fixed

  • #742 - Fix output dirs (HaplotypeCaller that was not recognized by annotate.nf introduced by #728)

[2.3] - Äpar - 2019-02-27

Added

  • #628, #722 - ASCAT now use .gc file
  • #712, #718 - Added possibilities to run Sarek with conda
  • #719 - Annotation documentation
  • #719 - Helper script to download snpeff and VEP cache files
  • #719 - New --annotation_cache, --snpEff_cache, --vep_cache parameters
  • #719 - Possibility to use cache wen annotating with snpEff and VEP
  • #722 - Add path to ASCAT .gc file in igenomes.config
  • #728 - Update Sarek-data submodule with multiple patients TSV file
  • #732 - Add cadd_WG_SNVs, cadd_WG_SNVs_tbi, cadd_InDels, cadd_InDels_tbi and cadd_cache params
  • #732 - Add tabix indexed cache for VEP
  • #732 - New DownloadCADD process to download CADD files
  • #732 - Specify values for cadd_WG_SNVs, cadd_WG_SNVs_tbi, cadd_InDels, cadd_InDels_tbi and cadd_cache params in munin.conf file
  • #732 - Use cadd_cache param for optional use of CADD VEP plugin in annotate.nf
  • #732 - VEP cache has now fasta files for --HGVS
  • #735 - Added --exome for Manta, and for StrelkaBP
  • #735 - Added Travis CI test for targeted

Changed

  • #710 - Improve release checklist and script
  • #711 - Improve configuration priorities
  • #716 - Update paths to containers and iGenomes
  • #717 - checkFileExtension has changed to hasExtension, and now only verify if file has extension
  • #717 - fastqFiles renamed to inputFiles
  • #717 - mapping step can now map BAM files too
  • #717 - MapReads can now convert BAM to FASTQ and feed it to BWA on the fly
  • #717, #732 - Update documentation
  • #719 - snpeff and vep containers are now built with conda
  • #719 - vepCacheVersion is now defined in conf/genomes.config or conf/igenomes.config
  • #722 - Add path to ASCAT .gc file in igenomes.config
  • #722 - Update Sarek-data submodule
  • #723, #725 - Update docs
  • #724 - Improved AwsBatch configuration
  • #728 - Improved usage of targetBED params
  • #728 - Strelka Best Practices output is now prefixed with StrelkaBP_
  • #728 - VCFs and Annotated VCFs are now ordered by Patient, then tools
  • #732 - Merge buildContainers.nf and buildReferences.nf in build.nf
  • #732 - Reduce number of CPUs for RunVEP to 4 cf: VEP docs
  • #732 - Update VEP from 95.1 to 95.2

Removed

  • #715 - Remove defReferencesFiles function from buildReferences.nf
  • #719 - snpEff base container is no longer used
  • #721 - Remove COSMIC docs
  • #728 - Remove defineDirectoryMap()
  • #732 - Removed --database option for VEP cf: VEP docs

Fixed

  • #720 - bamQC is now run on the recalibrated bams, and not after MarkDuplicates
  • #726 - Fix Ascat ref file input (one file can't be a set)
  • #727 - bamQC outputs are no longer overwritten (name of dir is now the file instead of sample)
  • #728 - Fix issue with annotation that was consuming cache channels
  • #728 - Fix multi sample TSV file #691
  • #733 - Fix the possibility to specify reference files on the command line

[2.2.2] - 2018-12-19

Added

  • #671 - New publishDirMode param and docs
  • #673, #675, #676 - Profiles for BinAC and CFC clusters in Tübingen
  • #679 - Add container for CreateIntervalBeds
  • #692, #697 - Add AWS iGenomes possibilities (within conf/igenomes.conf)
  • #694 - Add monochrome and grey logos for light or dark background
  • #698 - Add btb profile for munin server
  • #702 - Add font-ttf-dejavu-sans-mono 2.37 and fontconfig 2.12.6 to container

Changed

  • #663 - Update do_release.sh script
  • #671 - publishDir modes are now params
  • #677, #698, #703 - Update docs
  • #678 - Changing VEP to v92 and adjusting CPUs for VEP
  • #679 - Update old awsbatch configuration
  • #682 - Specifications for memory and cpus for awsbatch
  • #693 - Qualimap bamQC is now ran after mapping and after recalibration for better QC
  • #700 - Update GATK to 4.0.9.0
  • #702 - Update FastQC to 0.11.8
  • #705 - Change --TMP_DIR by --tmp-dir for GATK 4.0.9.0 BaseRecalibrator
  • #706 - Update TravisCI testing

Fixed

  • #665 - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the MarkDuplicates process, so metrics too
  • #672 - process PullSingularityContainers from buildContainers.nf now expect a file with the correct .simg extension for singularity images, and no longer the .img one.
  • #679 - Add publishDirMode for germlineVC.nf
  • #700 - Fix #699 missing DP in the FORMAT column VCFs for MuTect2
  • #702 - Fix #701
  • #705 - Fix #704

[2.2.1] - 2018-10-04

Changed

Fixed

  • #657 - Fix RunMultiQC.nf bug
  • #659 - Fix bugs due to updating Nextflow

[2.2.0] - Skårki - 2018-09-21

Added

  • #613 - Add Issue Templates (bug report and feature request)
  • #614 - Add PR Template
  • #615 - Add presentation
  • #616 - Update documentation
  • #620 - Add tmp/ to .gitignore
  • #625 - Add pathfindr as a submodule
  • #635 - To process targeted sequencing with a target BED
  • #639 - Add a complete example analysis to docs
  • #640, #642 - Add helper script for changing version number

Changed

  • #608 - Update Nextflow required version
  • #615 - Use splitCsv instead of readlines
  • #616 - Update CHANGELOG
  • #621, #638 - Improve install script
  • #621, #638 - Simplify tests
  • #627, #629, #637 - Refactor docs
  • #629 - Refactor config
  • #632 - Use 2 threads and 2 cpus FastQC processes
  • #637 - Update tool version gathering
  • #638 - Use correct .simg extension for Singularity images
  • #639 - Smaller refactoring of the docs
  • #640 - Update RELEASE_CHECKLIST
  • #642 - MultiQC 1.5 -> 1.6
  • #642 - Qualimap 2.2.2a -> 2.2.2b
  • #642 - Update conda channel order priorities
  • #642 - VCFanno 0.2.8 -> 0.3.0
  • #642 - VCFtools 0.1.15 -> 0.1.16

Removed

  • #616 - Remove old Issue Template
  • #629 - Remove old Dockerfiles
  • #637 - Remove old comments

Fixed

  • #621 - Fix VEP tests
  • #637 - Fix links in MD files

[2.1.0] - Ruotes - 2018-08-14

Added

  • #555 - snpEff output into VEP
  • #556 - Strelka Best Practices
  • #563 - Use SnpEFF reports in MultiQC
  • #568 - VCFTools process RunVcftools for QC
  • #574, #580 - Abstracts for NPMI, JOBIM and EACR25
  • #577 - New repository for testing: Sarek-data
  • #595 - New library QC for functions bamQC, bcftools, samtoolsStats, vcftools, getVersionBCFtools, getVersionGATK, getVersionManta, getVersionSnpEFF, getVersionStrelka, getVersionVCFtools, getVersionVEP
  • #595 - New Processes GetVersionBCFtools, GetVersionGATK, GetVersionManta, GetVersionSnpEFF, GetVersionStrelka, GetVersionVCFtools, GetVersionVEP
  • #595 - new Python script bin/scrape_tool_versions.py inspired by @ewels and @apeltzer
  • #595 - New QC Process RunVcftools
  • #596 - New profile for BinAC cluster
  • #597 - New function sarek_ascii() in SarekUtils
  • #599, #602 - New Process CompressVCF
  • #601, #603 - Container for GATK4
  • #606 - Add test data as a submodule from Sarek-data
  • #608 - Add documentation on how to install Nextflow on bianca

Changed

  • #557, #583, #585, #588 - Update help
  • #560 - GitHub langage for the repository is now Nextflow
  • #561 - do_all.sh build only containers for one genome reference (default GRCh38) only
  • #571 - Only one container for all QC tools
  • #582, #587 - Update figures
  • #595 - Function defineDirectoryMap() is now part of SarekUtils
  • #595 - Process GenerateMultiQCconfig replace by function createMultiQCconfig()
  • #597 - extractBams() now takes an extra parameter.
  • #597 - Move checkFileExtension(), checkParameterExistence(), checkParameterList(), checkReferenceMap(), checkRefExistence(), extractBams(), extractGenders(), returnFile(), returnStatus() and returnTSV() functions to SarekUtils
  • #597 - Reduce data footprint for Process CreateRecalibrationTable
  • #597 - Replace depreciated operator phase by join.
  • #599 - Merge is tested with ANNOTATEALL
  • #604 - Synching GRCh38 wgs_calling_regions bedfiles
  • #607 - One container approach
  • #607 - Update to GATK4
  • #608 - Update Nextflow required version
  • #616 - Update CHANGELOG
  • #617 - Replace depreciated $name syntax with withName

Fixed

  • #560 - Display message for repository and containerPath
  • #566 - slurmDownload profile
  • #579, #584 - Manta output reorganized after modification for Strelka Best Practices process
  • #585 - Trace file is plain txt
  • #590, #593 - Fix Singularity installation in Travis CI testing
  • #598, #601 - Fixes for Python script selectROI.py to work with CLC viewer

Removed

  • #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

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 - use Nextflow support of scratch
  • reordered Travis CI tests
  • update documentation
  • MultiQC version in container from v1.4 to v1.5
  • 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 v90 to v91
  • 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

  • #530 - use $PWD for default outDir
  • #533 - Replace VEP --pick option by --per_gene

[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

  • #488 - Better CPU requirements for ConcatVCF
  • #489 - Exception handling for ASCAT
  • #490 - CPU requirements for runSingleStrelka and runSingleManta

[1.2.3] - 2017-10-18

Fixed

  • #357 - ASCAT works for GRCh38
  • #471 - Running Singularity on /scratch
  • #475 - 16 cpus for local executor
  • #480 - No tsv file needed for step annotate

[1.2.2] - 2017-10-06

Fixed

  • #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

Removed

  • vep container
  • strelka_config.ini file

Fixed

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

[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