nf-core/sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

annotationcancergatk4genomicsgermlinepre-processingsomatictarget-panelsvariant-callingwhole-exome-sequencingwhole-genome-sequencing

Launch version 3.4.4 https://github.com/nf-core/sarek

Version history

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What’s Changed

FIX: misleading docs - xref 1621 by @maxulysse in #1623
Correct tower snpeff by @cmatKhan in #1627
Allow dbsnp if null in germline variant calling by @cmatKhan in #1628

New Contributors

@cmatKhan made their first contribution in #1627

Full Changelog: 3.4.3…3.4.4

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What’s Changed

Added

Add support for fastq.gz.spring-files as input by @asp8200 in [#1534, https:](https://github.com/nf-core/sarek/pull/1534, https:)//github.com/nf-core/sarek/pull/1573
Add a specific cnvkit/call module to perform calling from cns files by @lescai in #1502
Adds the cnvkit/export module, to export called CNVs into VCF by @lescai in #1502

Changed

Template update for nf-core/tools v2.14.1
Unify handling of params.cnvkit_reference uniform across the three subworkflows (germline, tumour only, tumour-normal) by @lescai in #1502
Simplify logic in args management by @maxulysse in #1521
Update vep cache version to 111 by @maxulysse in #1557
Cleanup + update modules by @maxulysse in #1545
Updating documentation by @asp8200 in [#1556 and by @maxulysse in https:](https://github.com/nf-core/sarek/pull/1556 and by @maxulysse in https:)//github.com/nf-core/sarek/pull/1570

Fixed

FIX: mapped bam and bai published in the same folder by @asp8200 in #1541
FIX: typo (strelka2 -> strelka) by @maxulysse in #1536
FIX: Typo build_from_index -> build_only_index by @maxulysse in #1547
FIX: Correct vep_cache_path_full when refseq/merged option is present by @YeHW in #1563
Remove snapshot from Haplotypecaller tests by @maxulysse in #1596
Remove snapshot from Deepvariant tests by @maxulysse in #1597
Remove empty outdirs by @FriederikeHanssen in #1612
Remove legacy configs of CUSTOM_DUMPSOFTWAREVERSIONS by @asp8200 in #1542

New Contributors

@famosab made their first contribution in #1527
@YeHW made their first contribution in #1563

Full Changelog: 3.4.2…3.4.3

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What’s Changed

3.5.0dev - back to dev by @maxulysse in #1477
feat(nf-prov): pin nf-prov to 1.2.2 by @maxulysse in #1482
Improve cloud testing matrix strategy by @adamrtalbot in #1378
Add new citation by @FriederikeHanssen in #1485
Fixing call to GATK4_HAPLOTYPECALLER by @asp8200 in #1488
Update sentieon modules to 202308.02 by @asp8200 in #1487
add test data in igenomes by @maxulysse in #1489
Update mosdepth by @asp8200 in #1490
feat(wave): add wave profile by @maxulysse in #1493
handle multiple DOIs by @maxulysse in #1496
Fix: Cloud Storage objects are immutable on GCP by @maxulysse in #1494
feat(release): prepare release 3.4.2 by @maxulysse in #1498
fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests by @maxulysse in #1499
fix: remove string none option from params.ascat_genome by @kenibrewer in #1501
Adding Simon and Ken by @maxulysse in #1509
Update CITATIONS.md with fgbio by @nh13 in #1505
fix(TYPO): index_alignement should be index_alignment by @nh13 in #1506
Release 3.4.2 by @maxulysse in #1484

New Contributors

@kenibrewer made their first contribution in #1501
@nh13 made their first contribution in #1505

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

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What’s Changed

Ncbench by @FriederikeHanssen in #1266
Back to Dev by @FriederikeHanssen in #1333
remove extra v for slack report by @FriederikeHanssen in #1334
add docs for bcftools annotate params by @FriederikeHanssen in #1335
Update sentieon-modules by @asp8200 in #1339
enable qc when starting from VC by @FriederikeHanssen in #1344
Preserve STDERR by @sminot in #1345
fix params in test profiles by @maxulysse in #1351
Add Azure megatests by @adamrtalbot in #1340
Important! Template update for nf-core/tools v2.11 by @nf-core-bot in #1360
1357 grouping strategy applied by counting number of FASTQ files generated by FASTP by @adamrtalbot in #1364
Template update for nf-core/tools version 2.11.1 by @mirpedrol in #1365
remove params from subworkflows by @maxulysse in #1359
Add test profile for ncbench by @FriederikeHanssen in #1372
fix intervals file by @FriederikeHanssen in #1373
Ncbench by @FriederikeHanssen in #1272
Ngscheckmate fix by @SPPearce in #1381
Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #1385
Update README.md by @maxulysse in #1390
Fix --three_prime_clip_r{1,2} parameter documentation (fixes #1382) by @tdanhorn in #1383
Updating sentieon modules by @asp8200 in #1401
fix dead link by @allaway in #1395
Fix intervals with dot by @maxulysse in #1403
add modules_testdata_base_path by @maxulysse in #1409
update triggered tests by @maxulysse in #1411
Updating samtools by @asp8200 in #1408
Update mulled-containers to samtools v1.19.2 by @asp8200 in #1412
Where is Edmund? by @maxulysse in #1413
Important! Template update for nf-core/tools v2.13 by @nf-core-bot in #1414
Fix test name by @maxulysse in #1407
updating GATK by @asp8200 in #1419
Removing docker.userEmulation by @asp8200 in #1405
Make -a a default argument for bcftools concat by @MatthiasZepper in #1420
ASSESS_SIGNIFICANCE fails with Rscript error fix by @nschcolnicov in #1400
Template update for nf-core/tools version 2.13.1 by @maxulysse in #1428
Fix datapath in nftests by @asp8200 in #1426
Using process.containerOptions instead of docker.runOptions by @asp8200 in #1431
Dummy PR : testing docker container options in GATK Spark modules by @asp8200 in #1430
Replacing local module BUILD_INTERVALS with nf-core mdule GAWK by @asp8200 in #1439
Light refactoring by @maxulysse in #1422
fix(spark): add a spark profile to set up the docker runOptions by @maxulysse in #1456
Removing stub option from nf-cmd in the test of pipeline-download by @asp8200 in #1436
feat(modules): update all modules by @maxulysse in #1457
prepare 3.4.1 by @maxulysse in #1461
Ascat fix by @maxulysse in #1462
fix(CI): add spark profile to all spark tests by @maxulysse in #1463
Fix call to SENTIEON_DEDUP by @asp8200 in #1465
feat(modules): update vep to 111.0 by @maxulysse in #1466
Fixing sentieon - code and tests by @asp8200 in #1469
Multiqc channels by @maxulysse in #1470
fix(schema): add some params to validationSchemaIgnoreParams for better handling by @maxulysse in #1471
fix(vep_cache_version-snpeff_db): both params are string by @maxulysse in #1472
fix(spark): load spark profile after loading the test profiles by @maxulysse in #1473
Release 3.4.1 by @maxulysse in #1460

New Contributors

@sminot made their first contribution in #1345
@mirpedrol made their first contribution in #1365
@tdanhorn made their first contribution in #1383
@allaway made their first contribution in #1395
@MatthiasZepper made their first contribution in #1420
@nschcolnicov made their first contribution in #1400

Full Changelog: 3.4.0…3.4.1

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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

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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

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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

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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

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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

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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

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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

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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

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What’s Changed

Release 3.1.2 by @maxulysse in #906

Full Changelog: 3.1.1…3.1.2

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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

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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

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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

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What’s Changed

Fix usage of intervals in samtools/mpileup by @nickhsmith in #708

Full Changelog: 3.0…3.0.1

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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

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What’s Changed

Fix MapReads caching bug by @BrunoGrandePhD in #566

Full Changelog: 2.7.1…2.7.2

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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