What’s Changed

New tools:

• Dnascope was added by @asp8200 in [#1193, https:](https://github.com/nf-core/sarek/pull/1193, https:)//github.com/nf-core/sarek/pull/1280
• Add NGSCheckMate by @SPPearce in #1252
• Add CnvkKt Genemetrics by @grantn5 in #1223
• Add Bcftools annotate by @grantn5 in #1267

Refactoring

• Add an nf-test CI by @adamrtalbot in [#1288, https:](https://github.com/nf-core/sarek/pull/1288, https:)//github.com/nf-core/sarek/pull/1289, #1290
• Created subworkflow for parsing samplesheet with nf-test by @RaqManzano in #1286
• Update config files and other minor code polishing by @maxulysse in #1325

Bug fixes and other updates

• Fix bug with params.json file writing on s3 by @FriederikeHanssen in #1318
• Fix links to docs by @maxulysse in #1328
• Fix nf-prov usage by @maxulysse in #1301
• Fix remove use_annotation_cache_keys params by @maxulysse in #1298
• Fix clashes of config of FILTERVARIANTTRANCHES in different subworkflows by @asp8200 in #1315
• Fix several bugs for joint calling with Mutect2 by @FriederikeHanssen & @maxulysse in [#1277, https:](https://github.com/nf-core/sarek/pull/1277, https:)//github.com/nf-core/sarek/pull/1309
• Update modules by @maxulysse & @FriederikeHanssen in [#1304, https:](https://github.com/nf-core/sarek/pull/1304, https:)//github.com/nf-core/sarek/pull/1311, #1327
• Add SnpEff to full sized tests by @FriederikeHanssen in #1330
• Proper usage of vep_version by @maxulysse in #1303
• Update docs by @FriederikeHanssen in [#1278, https:](https://github.com/nf-core/sarek/pull/1278, https:)//github.com/nf-core/sarek/pull/1317
• Adding labels to the local modules by @asp8200 in #1287

New Contributors

• @grantn5 made their first contribution in #1223
• @RaqManzano made their first contribution in #1286
• @SPPearce made their first contribution in #1252

Full Changelog: 3.3.2…3.4.0

What’s Changed

• back to dev by @FriederikeHanssen in #1246
• fix result path by @FriederikeHanssen in #1247
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #1254
• FIX: remove spaces in controlfreec modules by @maxulysse in #1256
• FEAT: Improve documentation for annotation cache by @maxulysse in #1248
• Add nf-prov by @maxulysse in #1259
• FEAT: add merge to cache checks by @maxulysse in #1261
• FEAT: prepare RC 3.3.2 by @maxulysse in #1262
• FIX: revert controlfreec-assesssignificance by @maxulysse in #1270
• FEAT: Release Canditate 3.3.2 by @maxulysse in #1264

Full Changelog: 3.3.1…3.3.2

What’s Changed

• FIX: Zenodo ID in manifest by @FriederikeHanssen in #1232
• FIX: Remove check annotation folders existence when no annotation by @maxulysse in #1236
• FIX: Disable JVM hotspot in gatk4 modules by @maxulysse in #1240
• UPDATE: Controlfreec version to 11.6b by @FriederikeHanssen in #1241
• FEAT: Improve schema usage for input by @maxulysse in #1243
• Simplify sentieon test license server usage by @maxulysse in #1242

Full Changelog: 3.3.0…3.3.1

What’s Changed

• FEAT: Mutect2 multi sample subworkflow by @berguner in #1013
• FEAT: Sentieon DNAseq workflow by @asp8200 in [#994. https:](https://github.com/nf-core/sarek/pull/994. https:)//github.com/nf-core/sarek/pull/1002. [#1007. https:](https://github.com/nf-core/sarek/pull/1007. https:)//github.com/nf-core/sarek/pull/1123. #1044.
• FEAT: Greatly improve tower.yml file by @maxulysse in #1197
• FEAT: Use annotation-cache and update VEP to v110 by @maxulysse in #1122
• FEAT: Added nf-validation for samplesheet validation by @mirpedrol in #1059
• Update of nf-core modules. [#1180. https:](https://github.com/nf-core/sarek/pull/1180. https:)//github.com/nf-core/sarek/pull/1160. [#1174. https:](https://github.com/nf-core/sarek/pull/1174. https:)//github.com/nf-core/sarek/pull/1227. #1224
• Improved docs. [#1163. https:](https://github.com/nf-core/sarek/pull/1163. https:)//github.com/nf-core/sarek/pull/1138 (@rhagenson), [#1192 (@JohannesKersting). https:](https://github.com/nf-core/sarek/pull/1192 (@JohannesKersting). https:)//github.com/nf-core/sarek/pull/1222 (@adamrtalbot). [#1166. https:](https://github.com/nf-core/sarek/pull/1166. https:)//github.com/nf-core/sarek/pull/1179 (@robsyme). #1183.
• snpeff_db parameter validation by @maxulysse in #1143
• FIX: Exome flag for Manta by @maxulysse in #1149
• FIX: Move all vep args from ext.args to params.vep_custom_args by @maxulysse in #1157
• FIX: GenomicsDB bug with mismatched intervals, remove duplicated variants from VQSR vcfs, add VQSR CI test by @FriederikeHanssen in #1173
• FIX: Improved workflows for GHA by @adamrtalbot in #1200
• FIX: Remove Nextflow caching for CI-tests by @Emiller88 in #1202
• FIX: Remove singularity tests from GHA by @maxulysse in #1218
• FIX: Better coverage for all tests by @maxulysse in [#1225, https:](https://github.com/nf-core/sarek/pull/1225, https:)//github.com/nf-core/sarek/pull/1216
• FIX: GVCF-files are published also when all intervals are processed at once by @FriederikeHanssen in #1172
• FIX: Don’t pass in intervals file to control-freec for WGS by @FriederikeHanssen in #1214
• FIX: getpileupsummary should not run if no germline resource is provided by @FriederikeHanssen in #1171

New Contributors

• @nicorap made their first contribution in #1111
• @rhagenson made their first contribution in #1138
• @berguner made their first contribution in #1013
• @mirpedrol made their first contribution in #1059
• @ATpoint made their first contribution in #1166
• @JohannesKersting made their first contribution in #1192

Full Changelog: 3.2.3…3.3.0

What’s Changed

• FIX: Remove public_aws_ecr profile by @maxulysse in #1118
• FIX: Remove default null in schema by @maxulysse in #1119
• CHORES: Prepare 3.2.3 by @asp8200 in #1128
• Release candidate 3.2.3 by @asp8200 in #1129

Full Changelog: 3.2.2…3.2.3

What’s Changed

• FIX: Fix default memory issue with gatk4/createsequencedictionary by @maxulysse in #1087
• Fix ascat manual test by @asp8200 in #1093
• FIX: Mutect2 subworkflow by @maxulysse in #1098
• FIX: Deepvariant duplicate index by @maxulysse in #1100
• FIX: Remove params.tracedir by @maxulysse in #1105
• FEAT: Add slack notification for megatests by @maxulysse in #1106
• Remove redundant index computation for MD & version for MD Spark by @FriederikeHanssen in #1101
• update config by @maxulysse in #1107
• fix bcftools mpileup by @FriederikeHanssen in #1109

Full Changelog: 3.2.1…3.2.2

What’s Changed

• CHORES: back to dev by @maxulysse in #1073
• fix typo in profile name by @maxulysse in #1079
• FIX: update bgziptabix module by @maxulysse in #1078
• CHORES: Prepare release 3.2.1 by @maxulysse in #1080
• FIX: patch more modules by @maxulysse in #1082
• Release candidate 3.2.1 by @maxulysse in #1081

Full Changelog: 3.2.0…3.2.1

What’s Changed

• Back to dev by @maxulysse in #859
• replace local subworkflow with nf-core version - vcf_annotate_snpeff by @maxulysse in #860
• switch mpileup to bcftools and subset to non-ref by @nickhsmith in #832
• add realigned bam export possibilities to gatk4_haplotypecaller by @maxulysse in #864
• fix bam output for haplotypecaller by @maxulysse in #870
• replace local subworkflow with nf-core version - vcf_annotate_ensemblvep by @maxulysse in #865
• nf-core modules update -a by @maxulysse in #874
• Concatenating germline vcfs by @asp8200 in #792
• Merging template updates 2.7.1 by @FriederikeHanssen in #890
• Important! Template update for nf-core/tools v2.7.1 by @nf-core-bot in #886
• default results should be null (fails on s3) by @maxulysse in #884
• Add skip_tools haplotypecaller_filter by @maxulysse in #889
• Remote test warning from nf-core lint by @maxulysse in #894
• Fix logic of when to execute tabix on dbsnp by @maxulysse in #893
• merge TEMPLATE by @maxulysse in #898
• Cache test data on GHA by @maxulysse in #909
• Refactor codebase - Part I by @maxulysse in #896
• Fix tumor only for freebayes by @maxulysse in #927
• Fix pair variant calling issue with msisensor by @maxulysse in #929
• Add build_only_index flag by @maxulysse in #935
• Add option to download cache for annotation by @maxulysse in #936
• FIX: Json validation for lists of tools by @maxulysse in #941
• FEAT: Update README by @maxulysse in #942
• Add Adam Talbot to contributor list by @FriederikeHanssen in #945
• Fix missing annotation keys for vep/snpeff by @maxulysse in #954
• Add failsafe options for Nextflow join operator by @maxulysse in #957
• update paths by @FriederikeHanssen in #965
• ADD: Annotation cache usage docs by @maxulysse in #967
• Don’t mutate channel elements in-place by @robsyme in #971
• Issue 950: samplesheet validation - no spaces in sample or patient names by @matrulda in #978
• ASCAT exome/targeted sequencing resource file generation by @ameynert in #981
• Remove exit statements by @FriederikeHanssen in #982
• ADD: Cache correctly identifies when it needs to be updated by @maxulysse in #985
• Updated ascat for reproducibility by @SusiJo in #988
• Issue 952 by @FriederikeHanssen in #998
• No need for BAI when using uBAM by @maxulysse in #928
• CHORE: update all modules by @maxulysse in #968
• CHORES: update subworkflows by @maxulysse in #1009
• CHORES: update TEMPLATE with 2.8 by @maxulysse in #1011
• Important! Template update for nf-core/tools v2.8 by @nf-core-bot in #1010
• fix genome null with annotation by @maxulysse in #1014
• Reduce interval groups default for smaller storage consumption by @FriederikeHanssen in #1015
• Set a default registry outside of profile scope by @maxulysse in #1019
• Fix input channels for variantrecalibrator by @asp8200 in #1022
• Update pipeline overview by @adamrtalbot in #1031
• refactoring by @maxulysse in #1012
• update all modules for correct registry usage by @maxulysse in #1032
• Remove concatenate_vcfs tests with singularity by @maxulysse in #1039
• FIX: dict channel issue when using params.dict by @maxulysse in #1040
• ADD: new vep_custom_args by @maxulysse in #1041
• FIX: typos by @maxulysse in #1043
• Adds public_aws_ecr profile for using ECR hosted images. by @adamrtalbot in #1045
• Input validation fixes by @FriederikeHanssen in #1048
• CHORES: modules update by @maxulysse in #1051
• Disable GATK filters when joint calling by @amizeranschi in #1050
• FIX: VCFTOOLS public ecr registry by @maxulysse in #1058
• CHORES: bump to 3.2.0 by @maxulysse in #1056
• remove exit strategy for MANTA/STRELKA by @maxulysse in #882
• FIX: pattern for fasta file by @maxulysse in #1055
• FIX: automatic restart from step by @maxulysse in #1062
• FIX: join duplication for manta/strelka annotation by @maxulysse in #1063
• don’t publish genomicsdb files by @FriederikeHanssen in #1061
• CHORES: remove version from pictures by @maxulysse in #1070
• docs update by @FriederikeHanssen in #1071
• Candidate release 3.2.0 by @maxulysse in #1057

New Contributors

• @robsyme made their first contribution in #971
• @matrulda made their first contribution in #978
• @ameynert made their first contribution in #981
• @adamrtalbot made their first contribution in #1031
• @amizeranschi made their first contribution in #1050

Full Changelog: 3.1.2…3.2.0

What’s Changed

• Release 3.1.2 by @maxulysse in #906

Full Changelog: 3.1.1…3.1.2

What’s Changed

• Syn up dev by @maxulysse in #849
• Remove “None” definition from schema by @drpatelh in #851
• Md cram update by @FriederikeHanssen in #855
• Add R64-1-1 and UMD3.1 by @maxulysse in #856
• prepare release 3.1.1 by @maxulysse in #858
• release 3.1.1 by @maxulysse in #857

Full Changelog: 3.1…3.1.1

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, https:](https://github.com/nf-core/sarek/pull/685, https:)//github.com/nf-core/sarek/pull/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, https:](https://github.com/nf-core/sarek/pull/736, https:)//github.com/nf-core/sarek/pull/691
• Clean up publishing by @FriederikeHanssen and @maxulysse in [#741, https:](https://github.com/nf-core/sarek/pull/741, https:)//github.com/nf-core/sarek/pull/705, #681
• Additional input checks by @asp8200 in #742
• Test profiles separated into multiple files to support usage with tower by @maxulysse in [#743, https:](https://github.com/nf-core/sarek/pull/743, https:)//github.com/nf-core/sarek/pull/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

• 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