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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.

2.7.2 - Áhkká

Áhkká is one of the massifs just outside of the Sarek National Park.

Fixed

  • #566 - Fix caching bug affecting a variable number of MapReads jobs due to non-deterministic state of statusMap during caching evaluation

2.7.1 - Pårtejekna

Pårtejekna is one of glaciers of the Pårte Massif.

Added

  • #353 - Add support for task retries with exit code 247 (exhibited by Picard MarkDuplicates)
  • #354 - Add tumor only mode for Mutect2 and MSIsensor
  • #356 - Add --cf_contamination_adjustment params to adjust contamination with Control-FREEC
  • #372 - Add --cf_contamination params to specify contamination value with Control-FREEC

Changed

  • #373 - Sync TEMPLATE with tools 1.14
  • #376 - Better logo on Github dark Mode
  • #387 - Fix tables for TSV file content

Fixed

  • #375, #381, #382, #385 - Fix bugs due to TEMPLATE sync from #373
  • #378 - Fix Spark related issue due to Docker settings in nextflow.config
  • #378 - Fix Spark related issue due to Docker settings in nextflow.config

Deprecated

Removed

  • #368 - Remove social preview image to use GitHub OpenGraph

2.7 - Pårte

Pårte is one of the main massif in the Sarek National Park.

Added

  • #145 - Add UMI annotation and consensus functionality to Sarek
  • #230 - Add ignore_soft_clipped_bases option for GATK Mutect2 #218
  • #253 - Add UMI CI testing
  • #262 - Add nextflow_schema.json
  • #237, #282 - Add --aligner to choose between bwa and bwa-mem2
  • #294 - Add Troubleshooting section to docs/usage.md
  • #302, #304 - Add WES and tumor-only mode for Control-FREEC

Changed

  • #253, #255, #326, #329 - Update docs
  • #260, #262, #278, #322 - Sync with TEMPLATE updated from nf-core/tools 1.10.2
  • #262 - Update issue templates to fit the recommended community standards
  • #278, #322 - Refactor docs
  • #284 - Update F1000Research publication to version 2
  • #284 - Update Scilifelab logo
  • #317 - Update README.md (Add: QBiC + Friederike/Gisela)
  • #320 - Set MarkDuplicates MAX_RECORDS_IN_RAM to default value

Fixed

  • #229 - Fix Control-FREEC restart issue #225
  • #236 - Fix GATK Mutect2 typo issue #227
  • #271 - Fix ConcatVCF_Mutect2 SIGPIPE issue #268
  • #272 - Fix annotation --tools merge issue
  • #279 - Fix issue with --step prepare_recalibration #267
  • #280 - Use HTML codes instead of < and > in docs
  • #288 - Fix test_annotation profile
  • #289 - Random string added to extractFastqFromDir to avoid name collition
  • #290, #323 - Faster solving of Conda environment
  • #293 - Fix typo issue when printing infos #292
  • #309 - Fixed concatenation of many VCF files
  • #310 - Fix Github Actions not running after November 16, 2020 (deprecated Github Actions API #739
  • #329 - Simplify Control-FREEC usage
  • #331 - Replace spread operator by combine to remove Nextflow deprecation warning

Removed

  • #234 - Removing obsolete script #92
  • #262 - Removing deprecated params: annotateTools, annotateVCF, cadd_InDels, cadd_InDels_tbi, cadd_WG_SNVs, cadd_WG_SNVs_tbi, maxMultiqcEmailFileSize, noGVCF, noReports, noStrelkaBP, nucleotidesPerSecond, publishDirMode, sample, sampleDir, saveGenomeIndex, skipQC, snpEff_cache, targetBed
  • #262 - Removing warning message about deprecated and obsolete params
  • #324 - --no_gatk_spark is now removed, use --use_gatk_spark instead
  • #324 - --no_gvcf is now removed, use --generate_gvcf instead

2.6.1 - Gådokgaskatjåhkkå

Gådokgaskatjåhkkå is the highest peak in the Piellorieppe massif.

Changed

  • #208 - Merge changes from the release PR
  • #208 - Bump version to 3.0dev
  • #214 - Update GATK from 4.1.6.0 to 4.1.7.0
  • #219 - Added awsfulltest.yml GitHub Actions workflow
  • #222 - Bump version to 2.6.1 and minor release
  • #223 - Apply comments from the release PR

Fixed

  • #211 - Extend timeout for pushing to DockerHub for VEP containers
  • #212 - No AWS test on forks
  • #214 - Fix channels collision between Freebayes and GATK Mutect2 #200
  • #214 - Fix warning Invalid tag value for CreateIntervalBeds #209
  • #214 - Fix GATK Mutect2 issue #210
  • #219 - Updated awstest.yml GitHub actions workflow
  • #221 - Fix issue with tmp_dir in BaseRecalibrator process

2.6 - Piellorieppe

Piellorieppe is one of the main massif in the Sarek National Park.

Added

  • #76 - Add GATK Spark possibilities to Sarek
  • #87 - Add GATK BaseRecalibrator plot to MultiQC report
  • #115 - Add @szilvajuhos abstract for ESHG2020
  • #117 - Add Trim Galore possibilities to Sarek
  • #141 - Add containers for WBcel235
  • #150, #151, #154 - Add AWS mega test GitHub Actions
  • #153 - Add CNVkit possibilities to Sarek
  • #158 - Added ggplot2 version 3.3.0
  • #163 - Add MSIsensor in tools and container
  • #164 - Add --no_gatk_spark params and tests
  • #167 - Add --markdup_java_options documentation
  • #169 - Add RELEASE_CHECKLIST.md document
  • #174 - Add variant_calling.md documentation
  • #175 - Add Sentieon documentation
  • #176 - Add empty custom genome in genomes.config to allow genomes that are not in AWS iGenomes
  • #179, #201 - Add FreeBayes germline variant calling
  • #180 - Now saving Mapped BAMs (and creating TSV) in minimal setting
  • #182 - Add possibility to run HaplotypeCaller without dbsnp so it can be used to actually generate vcfs to build a set of known sites (cf gatkforums)
  • #195 - Now creating TSV for duplicates marked BAMs in minimal setting
  • #195, #202 - Add --save_bam_mapped params to save mapped BAMs.
  • #197 - Add step prepare_recalibration to allow restart from DuplicatesMarked BAMs
  • #204 - Add step Control-FREEC to allow restart from pileup files
  • #205 - Add --skip_markduplicates to allow skipping the MarkDuplicates process

Changed

  • #76 - Use MarkDuplicatesSpark instead of MarkDuplicates
  • #76 - Use gatk4-spark instead of gatk4 in environment.yml
  • #80 - Re-bump dev branch
  • #85 - Use new merged vcf files for known indels to simplify setting up channel
  • #104 - Update Figure 1
  • #107 - Switch params to snake_case
  • #109 - Update publication with F1000Research preprint
  • #113 - Move social preview image
  • #120 - Sync TEMPLATE
  • #121 - Update MultiQC to 1.8
  • #126, #131 - Update docs
  • #131 - Use nfcore/base:1.9 as base for containers
  • #131 - Update Control-FREEC to 11.5
  • #131 - Update FastQC to 0.11.9
  • #131 - Update FreeBayes to 1.3.2
  • #131 - Update Manta to 1.6.0
  • #131 - Update Qualimap to 2.2.2d
  • #131 - Update VEP to 99.2
  • #141 - Update snpEff cache version from 75 to 87 for GRCh37
  • #141 - Update snpEff cache version from 86 to 92 for GRCh38
  • #141 - Update VEP databases to 99
  • #143 - Revert snpEff cache version to 75 for GRCh37
  • #143 - Revert snpEff cache version to 86 for GRCh38
  • #152, #158, #164, #174, #194, #198, #204 - Update docs
  • #164 - Update gatk4-spark from 4.1.4.1 to 4.1.6.0
  • #180, #195 - Improve minimal setting
  • #183, #204 - Update input.md documentation
  • #197 - Output directory DuplicateMarked is now replaced by DuplicatesMarked
  • #204 - Output directory controlFREEC is now replaced by Control-FREEC

Fixed

  • #83 - Fix some typos in docs/input.md
  • #107 - Fix linting
  • #110 - Fix snpEff report issue cf #106
  • #126 - Fix iGenomes paths
  • #127, #128 - Fix ASCAT
  • #129 - Fix issue with Channel channel ch_software_versions_yaml
  • #129 - Apply @drpatelh fix for mardown_to_html.py compatibility with Python 2
  • #129 - Removed Python 3.7.3 from conda environment due to incompatibility
  • #129 - Change ascii characters that were not supported from the output.md docs
  • #140 - Fix extra T/N combinations for ASCAT cf #136
  • #141 - Fix download_cache.nf script to download cache for snpEff and VEP
  • #143 - Fix annotation CI testing with snpEff and VEP
  • #144 - Fix CircleCI for building VEP containers
  • #146 - Fix --no_intervals for GATK Mutect2 cf #135
  • #156 - Fix typos
  • #156 - Fix issues with dbsnp files while using only Sention tools
  • #158 - Fix typo with params.snpeff_cache to decide containers for snpEff
  • #164 - Fix issues when running with Sentieon
  • #164 - Add more VCFs to annotation
  • #167 - Add --markdup_java_options documentation to fix #166
  • #178 - Fix Sentieon variant calling, now using deduped bam files
  • #188 - Fix input/output channels for process IndexBamFile to match actual files in the mapped.tsv files
  • #189 - Fix no_intervals for process HaplotypeCaller (the file just need to actually exists...)
  • #197 - Fix issue with --step recalibrate
  • #197 - Fix typo in output directory DuplicateMarked -> DuplicatesMarked

Deprecated

  • #107 - --annotateTools is now deprecated, use --annotate_tools instead
  • #107 - --cadd_InDels is now deprecated, use --cadd_indels instead
  • #107 - --cadd_InDels_tbi is now deprecated, use --cadd_indels_tbi instead
  • #107 - --cadd_WG_SNVs is now deprecated, use --cadd_wg_snvs instead
  • #107 - --cadd_WG_SNVs_tbi is now deprecated, use --cadd_wg_snvs_tbi instead
  • #107 - --maxMultiqcEmailFileSize is now deprecated, use --max_multiqc_email_size instead
  • #107 - --noGVCF is now deprecated, use --no_gvcf instead
  • #107 - --noStrelkaBP is now deprecated, use --no_strelka_bp instead
  • #107 - --nucleotidesPerSecond is now deprecated, use --nucleotides_per_second instead
  • #107 - --publishDirMode is now deprecated, use --publish_dir_mode instead
  • #107 - --saveGenomeIndex is now deprecated, use --save_reference instead
  • #107 - --skipQC is now deprecated, use --skip_qc instead
  • #107 - --snpEff_cache is now deprecated, use --snpeff_cache instead
  • #107 - --targetBed is now deprecated, use --target_bed instead

Removed

  • #107 - --acLociGC is now removed, use --ac_loci_gc instead
  • #107 - --acLoci is now removed, use --ac_loci instead
  • #107 - --bwaIndex is now removed, use --bwa instead
  • #107 - --chrDir is now removed, use --chr_dir instead
  • #107 - --chrLength is now removed, use --chr_length instead
  • #107 - --dbsnpIndex is now removed, use --dbsnp_index instead
  • #107 - --fastaFai is now removed, use --fasta_fai instead
  • #107 - --genomeDict is now removed, use --dict instead
  • #107 - --genomeFile is now removed, use --fasta instead
  • #107 - --genomeIndex is now removed, use --fasta_fai instead
  • #107 - --germlineResourceIndex is now removed, use --germline_resource_index instead
  • #107 - --germlineResource is now removed, use --germline_resource instead
  • #107 - --igenomesIgnore is now removed, use --igenomes_ignore instead
  • #107 - --knownIndelsIndex is now removed, use --known_indels_index instead
  • #107 - --knownIndels is now removed, use --known_indels instead
  • #107 - --singleCPUMem is now removed, use --single_cpu_mem instead
  • #107 - --snpeffDb is now removed, use --snpeff_db instead
  • #107 - --vepCacheVersion is now removed, use --vep_cache_version instead
  • #152 - Removed Jenkinsfile
  • #169 - Removed omicX from README
  • #181 - Remove duplicate code in nextflow.config

2.5.2 - Jåkkåtjkaskajekna

Jåkkåtjkaskajekna is one of the two glaciers of the Ålkatj Massif.

Added

  • #45 - Include Workflow figure in README.md
  • #46 - Add location to abstracts
  • #52 - Add support for mouse data GRCm38
  • #60 - Add no_intervals params
  • #60 - Add automatic generation of intervals file with BuildIntervals process
  • #60 - Add minimal support for minimal genome (only fasta, or fasta + knownIndels)
  • #60 - Add new processes (IndexBamFile, IndexBamRecal) to deal with optional usage of interval files and minimal genome
  • #60 - Add tests for minimal genome usage
  • #60 - Add new minimal genomes (TAIR10, EB2, UMD3.1, bosTau8, WBcel235, ce10, CanFam3.1, canFam3, GRCz10, danRer10, BDGP6, dm6, EquCab2, equCab2, EB1, Galgal4, galGal4, Gm01, hg38, hg19, Mmul_1, mm10, IRGSP-1.0, CHIMP2.1.4, panTro4, Rnor_6.0, rn6, R64-1-1, sacCer3, EF2, Sbi1, Sscrofa10.2, susScr3, AGPv3) to igenomes.config
  • #61 - Add params split_fastq
  • #61 - Add test SPLITFASTQ
  • #66 - Add Sentieon possibilities to Sarek

Changed

  • #54 - Bump version to 2.5.2dev
  • #60 - Some process (BaseRecalibrator, ApplyBQSR, Mpileup) have now optional usage of interval files
  • #60 - Update documentation
  • #71 - Update README
  • #71 - Update CHANGELOG
  • #74 - Update docs
  • #74 - Improve CI tests (both Jenkins and GitHub actions tests)
  • #74 - Move all CI from ci-extra.yml to ci.yml

Removed

  • #46 - Remove mention of old build.nf script which was included in main.nf
  • #74 - Remove download_image.sh and run_tests.sh scripts
  • #76 - Remove runOptions = "-u \$(id -u):\$(id -g)" in nextflow.config to enable Spark possibilities

Fixed

  • #40 - Fix issue with publishDirMode within test profile
  • #42 - Fix typos, and minor updates in README.md
  • #43 - Fix automated VEP builds with circleCI
  • #54 - Apply fixes from release 2.5.1
  • #58 - Fix issue with .interval_list file from the GATK bundle #56 that was not recognized in the CreateIntervalsBed process
  • #71 - Fix typos in CHANGELOG
  • #73 - Fix issue with label memory_max for BaseRecalibrator process #72

2.5.1 - Årjep-Ålkatjjekna

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

Added

  • #53 - Release 2.5.1

Fixed

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

2.5 - Ålkatj

Ålkatj is one of the main massif in the Sarek National Park.

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, GATK 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 configuration 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 configuration
  • #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 VEP 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 - AWS iGenomes config now contains germline resource for GATK4 Mutect2
  • #30 - Simplify code for MapReads process
  • #24 - AWS 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 GATK 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

Äpar is one of the main massif in the Sarek National Park.

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 AWS 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 AWS batch 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 - Remove --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 2.1dev 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 Travis CI 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

Skårki is one of the main massif in the Sarek National Park.

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

Ruotes is one of the main massif in the Sarek National Park.

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 Nextflow ``$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

First release under the Sarek name, from the National Park in Northern Sweden

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