What's Changed

• Back to business on dev by @maxulysse in #762
• Update subway map by @FriederikeHanssen in #766
• Dev deepvariant by @maxulysse in #768
• Fix gatk4 cnnscorevariants by @maxulysse in #770
• add logo for Danish National Genome Center by @maxulysse in #774
• update to new modules syntax + patch on non-up to date modules by @maxulysse in #771
• nf core template merge 2.6 by @maxulysse in #773
• AWS outdir paths were mixed up by @FriederikeHanssen in #777
• Add this years posters by @FriederikeHanssen in #775
• use chr length file by default since cf is otherwise not working by @FriederikeHanssen in #783
• No scatter on full size tests to avoid issues with in or output files randomly not staged by @FriederikeHanssen in #782
• Updated docs of bcftools stats variant depth by @SusiJo in #788
• ci: Move tmpdir to ~ by @emiller88 in #791
• Fix somatic test with mutect2 by @SusiJo in #790
• Md cram by @FriederikeHanssen in #735
• don't annotate gvcfs by @FriederikeHanssen in #793
• Don't publish unzip files by @FriederikeHanssen in #794
• Update ci.yml by @maxulysse in #796
• Update all subworkflows name by @maxulysse in #784
• Fix sample header error when starting from bams by @FriederikeHanssen in #807
• More complete CI by @maxulysse in #806
• add rgid, to separate sample info by @FriederikeHanssen in #814
• Fix validation of input when launching from website by @FriederikeHanssen in #813
• collect cnvkit reference to not be consumed by @FriederikeHanssen in #817
• prioritze test conf for mutect in tests by @FriederikeHanssen in #815
• Use putIfAbsent by @FriederikeHanssen in #821
• add speed up parameters for genomicsdb by @FriederikeHanssen in #827
• Add option for cnvkit to provide external Cnn reference by @FriederikeHanssen in #825
• add more docs about scatter/gather by @FriederikeHanssen in #820
• Fix bug with no variantcalling when starting from step recalibration Issue 763 by @FriederikeHanssen in #828
• Update modules & tool versions by @FriederikeHanssen in #822
• Get ride of copyTo to enable s3 buckets in different regiosn by @maxulysse in #839
• remove cf len file from config by @FriederikeHanssen in #841
• increase samtools stats memory by @FriederikeHanssen in #842

Full Changelog: 3.0.2...3.1

What's Changed

• Fix Vep plugin usage by @BarryDigby in #688
• Fix when clause for building mapping indexes by @maxulysse in #689
• Updating nf-core-modules by @asp8200 in #685, #734
• Fix schema for controlfreec ploidy by @FriederikeHanssen in #704
• Vep Issues: loftee needs version by @FriederikeHanssen in #706
• Adding md5-sums to the test-yml-files by @asp8200 in #696
• sync 2.5 by @maxulysse in #720
• Dev sync 2.5.1 by @maxulysse in #723
• Subway update by @FriederikeHanssen in #719
• Add in Azure config documentation by @vsmalladi in #716
• Add further support ControlFreec for targeted data by @FriederikeHanssen in #728
• Allow interval.{bed,interval,interval_list} files by @FriederikeHanssen in #727
• Switch germline and somatic full tests by @FriederikeHanssen in #731
• Optimize resource requests by @FriederikeHanssen in #726
• Add testing for conda/singularity by @maxulysse in #736, #691
• Clean up publishing by @FriederikeHanssen and @maxulysse in #741, #705, #681
• Additional input checks by @asp8200 in #742
• Test profiles separated into multiple files to support usage with tower by @maxulysse in #743, #692
• Remove errorStrategy in modules.config by @drpatelh in #757
• update zenodo link to point to latest by @FriederikeHanssen in #758

New Contributors

• @BarryDigby made their first contribution in #688
• @vsmalladi made their first contribution in #715
• @drpatelh made their first contribution in #757

Full Changelog: 3.0.1...3.0.2

What's Changed

• Fix usage of intervals in samtools/mpileup by @nickhsmith in #708

Full Changelog: 3.0...3.0.1

• Porting to DSL2
• Use CRAM files where possible
• Add new tools: DragMap, DeepVariant, Joint germline calling, Haplotypecaller single sample, CNVKit Somatic, Tiddit Somatic
• Replaced tools: Trimgalore -> Fastp, Qualimap -> Mosdepth
• New references: BWAMem2, DragMap, Germline Resource
• Add a new entry --step markduplicates
• Steps can be started from bam or cram files
• Added --paired_variant_calling_only to skip normal computations for paired samples
• Only unmatched tumor samples will be run in single mode
• Input fastq files are split by default and mapped in parallel
• Bam2Fastq: changed to using samtools
• Samplesheet is now in CSV format with a header line with improved validation and flexibility
• New parameter --skip_tools retires --skip_qc, --skip_markduplicates and --skip_bqsr
• --sequencing_center renamed to --seq_platform`
• New parameter --wes must be set for targeted data
• New parameter --save_bam_ouput to store results file in BAM format instead of CRAM
• Additional VEP output formats
• Additional VEP plugins: loftee, spliceAI, spliceRegions, dbnsfp
• Remove sentieon support

New Contributors

• @abhi18av made their first contribution in #394
• @nickhsmith made their first contribution in #454
• @emiller88 made their first contribution in #465
• @priesgo made their first contribution in #432
• @SusiJo made their first contribution in #545
• @asp8200 made their first contribution in #571
• @lassefolkersen made their first contribution in #591
• @WackerO made their first contribution in #570

Full Changelog: 2.7.2...3.0

What's Changed

• Fix MapReads caching bug by @BrunoGrandePhD in #566

Full Changelog: 2.7.1...2.7.2

• Add tumor only mode for Mutect2 and MSIsensor
• Add --cf_contamination_adjustment params to adjust contamination with Control-FREEC (356)
• Add --cf_contamination params to specify contamination value with Control-FREEC (372)
• Sync TEMPLATE with tools 1.14 (#373)
• Fix Spark related issue due to Docker settings in nextflow.config

See full CHANGELOG, for more information

• Add UMI annotation and consensus functionality to Sarek (#145)
• Add ignore_soft_clipped_bases option for GATK Mutect2 (#230)
• Add --aligner to choose between bwa and bwa-mem2 (#237, #282)
• Add WES and tumor-only mode for Control-FREEC (#302, #304)
• Update Control-FREEC from 11.5 to 11.6
• --no_gatk_spark is now removed, use --use_gatk_spark if you want to use GATK Spark
• --no_gvcf is now removed, use --generate_gvcf if you want *.g.vcf files from GATK HaplotypeCaller

See full CHANGELOG, for more information

• Update GATK from 4.1.6.0 to 4.1.7.0 (#214)
• Fix channels collision between Freebayes and Mutect2 (#214)
• Fix Mutect2 issue #210 (#214)
• Add awsfulltest.yml GitHub Actions workflow (#219)

See full CHANGELOG, for more information

• Add GATK Spark possibilities (#76)
• Add CNVkit (#153)
• Add MSIsensor (#163)
• Improve support for minimal genome (only fasta)
• Output directory DuplicateMarked is now replaced by DuplicatesMarked
• Output directory controlFREEC is now replaced by Control-FREEC
• Fix annotation CI testing with snpEff and VEP (#143)
• Fix --no_intervals for Mutect2 (#146)
• Add --skip_markduplicates (#205)

See full CHANGELOG, for more information

• Add mouse (GRCm38) support (#52)
• Add minimal support for minimal genome (only fasta or fasta + knownIndels) (#60)
• Add new params split_fastq (#61)
• Fix issue with .interval_list file from the GATK bundle (#58)
• Fix issue with label memory_max for BaseRecalibrator process (#73)

See full CHANGELOG, for more information