Releases: nf-core/sarek
Releases · nf-core/sarek
Sarek 3.4.0 - Pårtetjåkko
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
Sarek 3.3.2 - Ráhpajávvre
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
Sarek 3.3.1 - Biellorippjávrre
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
Sarek 3.3.0 - Rapaselet
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-validationfor 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_dbparameter 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
Sarek 3.2.3 - Gällivare
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
Sarek 3.2.2 - Vuoinesluobbalah
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
Sarek 3.2.1 - Pierikjaure
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
Sarek 3.2.0 - Bierikjávrre
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
Sarek 3.1.2 - Lesser Lule River
Sarek 3.1.1 - Lilla Luleälven
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