Version history

What’s Changed

New Contributors

Full Changelog: 3.4.3…3.4.4

What’s Changed

Added

Changed

Fixed

New Contributors

Full Changelog: 3.4.2…3.4.3

What’s Changed

New Contributors

Full Changelog: 3.4.1…3.4.2

https://github.com/nf-core/sarek/blob/master/CHANGELOG.md#342---s%C3%A1jt%C3%A1ristj%C3%A5hkk%C3%A5

What’s Changed

New Contributors

Full Changelog: 3.4.0…3.4.1

What’s Changed

New tools:

Refactoring

Bug fixes and other updates

New Contributors

Full Changelog: 3.3.2…3.4.0

What’s Changed

Full Changelog: 3.3.1…3.3.2

What’s Changed

Full Changelog: 3.3.0…3.3.1

What’s Changed

New Contributors

Full Changelog: 3.2.3…3.3.0

What’s Changed

Full Changelog: 3.2.2…3.2.3

What’s Changed

Full Changelog: 3.2.1…3.2.2

What’s Changed

Full Changelog: 3.2.0…3.2.1

What’s Changed

New Contributors

Full Changelog: 3.1.2…3.2.0

What’s Changed

Full Changelog: 3.1.1…3.1.2

What’s Changed

Full Changelog: 3.1…3.1.1

What’s Changed

Full Changelog: 3.0.2…3.1

What’s Changed

New Contributors

Full Changelog: 3.0.1…3.0.2

What’s Changed

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

Full Changelog: 2.7.2…3.0

What’s Changed

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

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

See full CHANGELOG, for more information

  • First release within nf-core
  • Compliant within all nf-core requirements
    • One script to rule them all
    • Full AWS iGenomes support
  • Adds PON for Mutect2
  • Adds TIDDIT for Germline sample
  • Adds Control-FREEC for CNV
  • Change in parameter names:
    • sampleDir, sample and annotateVCF are now input
    • genomeFile is now fasta
    • genomeIndex is now fastaFai
    • genomeDict is now dict

See full CHANGELOG, for more information