What's Changed

New tools:

• Dnascope was added by @asp8200 in #1193, #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, #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, #1309
• Update modules by @maxulysse & @FriederikeHanssen in #1304, #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, #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. #1002. #1007. #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. #1160. #1174. #1227. #1224
• Improved docs. #1163. #1138 (@rhagenson), #1192 (@JohannesKersting). #1222 (@adamrtalbot). #1166. #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, #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