Sarek 2.7.1 - Pårtejekna

• 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

Sarek 2.7 - Pårte

• 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

Sarek 2.6.1 - Gådokgaskatjåhkkå

• 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

Sarek 2.6 - Piellorieppe

• 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

Sarek 2.5.2 - Jåkkåtjkaskajekna

• 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

Sarek 2.5.1 - Årjep-Ålkatjjekna

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

See full CHANGELOG, for more information

Sarek 2.5 - Ålkatj

• 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