CHANGELOG.md

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.

[Unreleased]

Changed

• #741 - Use dump operator
• #744 - Refactor germlineVC.nf
• #744 - Refactor germlineVC.nf
• #753 - Update binac, cfc configuration
• #775 - Update paths for munin configuration
• #776 - Helper script now download annotations for VEP CADD plugin
• #776 - Helper script now download annotations for VEP CADD plugin
• #778 - add || true for all tools when gathering versions
• #793 - Update munin configuration
• #798 - Can handle both fastq.gz and fq.gz

Added

• #766 - Added ps in r-base and runallelecount containers
• #774 - Autogenerates memory requirements from MarkDuplicates when less that 8G is available. cf nf-core/rnaseq#179
• #777 - Add removeVCF() function to remove .ann, .gz and .vcf from a VCF filename
• #777 - Add GeneSplicer 1.0 to container
• #777 - Add possibility to use VEP GeneSplicer plugin

Fixed

• #747 - Exclude Manta *candidateSV.vcf from annotation
• #749 - Fix config problematic use of queue core for uppmax-slurm
• #751, #756 - Typos in igenomes.config
• #757 - Typos in binac, cfc configuration
• #758 - Typos in ASCAT documentation
• #760 - Fix undefined task.mem
• #765 - Check only for references that are needed to fix #754
• #777 - Fix name collision in annotate.nf
• #788 - Fix genome_base path in munin.config
• #788 - Fix markdup_java_options definition
• #788 - Include conf/resources.config in btb profile
• #795 - Use BED file for QualiMap coverage calculation on Targeted Data
• #801 - Uppmax specific config fix for jobs not using a full node

Deprecated

• #741 - Deprecated verbose params

[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

• #646 - Update pathfindr submodule
• #659 - Update Nextflow to 0.32.0
• #660 - Update docs

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 deprecated 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 deprecated $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