nf-core/sarek: 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.

[2.5.1] - Årjep-Ålkatjjekna

Årjep-Ålkatjjekna is one of the two glaciers of the Ålkatj Massif.

`Fixed`

#48 - Fix singularity.autoMounts issue.
#49 - Use correct tag for annotation containers.
#50 - Fix paths for scripts.

[2.5] - Ålkatj

Initial release of nf-core/sarek, created with the nf-core template.

`Added`

#2 - Create nf-core/sarek environment.yml file
#2, #3, #4, #5, #7, #9, #10, #11, #12 - Add CI for nf-core/sarek
#3 - Add preprocessing to nf-core/sarek
#4 - Add variant calling to nf-core/sarek with HaplotypeCaller, and single mode Manta and Strelka
#5, #34 - Add variant calling to nf-core/sarek with Manta, Strelka, Strelka Best Practices, MuTecT2, FreeBayes, ASCAT, ControlFREEC
#6 - Add default containers for annotation to nf-core/sarek
#7 - Add MultiQC
#7 - Add annotation
#7 - Add social preview image in png and svg format
#7, #8, #11, #21 - Add helper script run_tests.sh to run different tests
#7, #8, #9 - Add automatic build of specific containers for annotation for GRCh37, GRCh38 and GRCm38 using CircleCI
#7, #8, #9, #11 - Add helper script build_reference.sh to build small reference from nf-core/test-datasets:sarek
#7, #9, #11, #12 - Add helper script download_image.sh to download containers for testing
#8 - Add test configation for easier testing
#9, #11 - Add scripts for ASCAT
#10 - Add TIDDIT to detect structural variants
#11 - Add automatic build of specific containers for annotation for CanFam3.1 using CircleCI
#11, #12 - Add posters and abstracts
#12 - Add helper script make_snapshot.sh to make an archive for usage on a secure cluster
#12 - Add helper scripts filter_locifile.py and selectROI.py
#12 - Use label for processes configation
#13 - Add Citation documentation
#13 - Add BamQC process
#13 - Add CompressVCFsnpEff and CompressVCFvep processes
#18 - Add --no-reports option for tests + add snpEff,VEP,merge to MULTIPLE test
#18 - Add logo to MultiQC report
#18, #29 - Add params --skipQC to skip specified QC tools
#18 - Add possibility to download other genome for sareksnpeff and sarekvep containers
#20 - Add markdownlint config file
#21 - Add tests for latest Nextflow version as well
#21 - Add genomes.config for genomes without AWS iGenomes
#24 - Added GATK4 Mutect2 calling and filtering
#27, #30 - Use Github actions for CI, linting and branch protection
#31 - Add nf-core lint
#31 - Add extra CI to GitHub Actions nf-core extra CI
#35 - Building indexes from nf-core/test-datasets:sarek for CI and small tests

`Changed`

#1, #2, #3, #4, #5, #6, #7, #8, #9, #10, #11, #12, #18, #20, #21, #23, #29 - Update docs
#4 - Update cancerit-allelecount from 2.1.2 to 4.0.2
#4 - Update gatk4 from 4.1.1.0 to 4.1.2.0
#7, #23 - --sampleDir is now deprecated, use --input instead
#7, #23 - --annotateVCF is now deprecated, use --input instead
#8, #12 - Improve helper script build.nf for downloading and building reference files
#9 - ApplyBQSR is now parallelized
#9 - Fastq files are named following "${idRun}_R1.fastq.gz" in the FastQC output for easier reporting
#9 - Status is now a map with idpatient, idsample as keys (ie: status = statusMap[idPatient, idSample])
#9 - Use ensembl-vep 95.2 instead of 96.0
#11 - Summary HTML from VWP is now in the Reports directory
#12 - Update configuration files
#12 - Disable Docker in singularity profile
#12 - Disable Singularity in docker profile
#12 - Disable Docker and Singularity in conda profile
#12 - Simplify check_max() function
#13 - Merge BamQCmapped and BamQCrecalibrated processes into BamQC process
#13 - Split CompressVCF process into CompressVCFsnpEff and CompressVCFvep processes
#16 - Make scripts in bin/ and scripts/ executable
#18 - Use --no-reports for TravisCI testing
#18 - Add --no-reports for all tests but MULTIPLE in Jenkins
#18, #29 - --noReports is now --skipQC all
#18, #21 - Update logo
#21 - Moved smallGRCh37 path to genomes.config
#23 - Rename genomeFile, genomeIndex and genomeDict by fasta, fastaFai and dict
#23 - --sample is now deprecated, use --input instead
#23 - --genomeFile is now deprecated, use --fasta instead
#23 - --genomeIndex is now deprecated, use --fastaFai instead
#23 - --genomeDict is now deprecated, use --dict instead
#24 - iGenomes config now contains germline resource for GATK4 Mutect2
#30 - Simplify code for MapReads process
#24 - iGenomes config now contains germline resource for GATK4 Mutect2
#31 - Move extra CI to GitHub Actions nf-core extra CI
#32, #33 - Install ASCAT with conda in the environment.yml file
#33 - use workflow.manifest.version to specify workflow version in path to scripts for ControlFREEC and VEP processes
#35 - Building indexes is now done in main.nf
#35 - build.nf script now only download cache, so renamed to downloadcache.nf
#35 - Use tabix instead of IGVtools to build vcf indexes
#35 - Refactor references handling
#35 - use Channel values instead of referenceMap
#37 - Bump version for Release
#38 - File names before merge is based on ${idSample}_${idRun} instead of ${idRun}

`Removed`

#9 - Removed relatedness2 graph from vcftools stats
#13 - Removed BamQCmapped and BamQCrecalibrated processes
#13 - Removed CompressVCF
#18 - Removed params --noReports
#24 - Removed GATK3.X MuTect2
#31 - Remove extra CI from Travis CI and GitHub Actions nf-core CI
#32, #35 - Clean up environment.yml file
#35 - Remove building indexes from build.nf script
#35 - Remove helper script build_reference.sh
#35 - Remove IGVtools
#35 - Remove Mutect2 from MULTIPLE test
#35 - Remove referenceMap and defineReferenceMap() and use Channel values instead

`Fixed`

#3 - Fix Docker ownership
#11 - Fix MergeMpileup PublishDir
#13 - Fix merge in annotation
#14 - Fix output name for vcf files
#16 - Fix path to Rscript
#18 - Improve cpu usage
#18 - Use same font for nf-core and sarek in ascii art
#20 - Use new logo in README
#20 - Fix path to references genomes
#22 - Fix --singleCPUMem issue
#30 - fix choice between inputPairReadsFastQC and inputBAMFastQC channels
#31 - Fix badges according to nf-core lint
#31 - Fix rcolorbrewer version according to nf-core lint
#33 - Fix MD Linting
#38 - Avoid collision in MultiQC
#39 - Fix ch_dbsnp channel

`Deprecated`

#23 - --sample is now deprecated, use --input instead
#23 - --genomeFile is now deprecated, use --fasta instead
#23 - --genomeIndex is now deprecated, use --fastaFai instead
#23 - --genomeDict is now deprecated, use --dict instead
#29 - --noReports is now deprecated, use --skipQC all

[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

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nf-core/sarek: Changelog

[2.5.1] - Årjep-Ålkatjjekna

Fixed

[2.5] - Ålkatj

Added

Changed

Removed

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Deprecated

[2.3.FIX1] - 2019-03-04

Fixed

[2.3] - Äpar - 2019-02-27

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[2.2.2] - 2018-12-19

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[2.2.1] - 2018-10-04

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[2.2.0] - Skårki - 2018-09-21

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[2.1.0] - Ruotes - 2018-08-14

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[2.0.0] - 2018-03-23

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[1.2.5] - 2018-01-18

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[1.2.4] - 2017-10-27

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[1.2.3] - 2017-10-18

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[1.2.2] - 2017-10-06

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[1.2.1] - 2017-10-06

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[1.2.0] - 2017-10-02

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[1.1] - 2017-09-15

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[1.0] - 2017-02-16

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[0.9] - 2016-11-16

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[0.1] - 2016-04-05

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