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 3.6.1 https://github.com/nf-core/sarek

Version history

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What’s Changed

This release contains a fix for --aligner parabricks to use the correct intervals channel when running with --wes or --intervals <file> see #2029.

This patch release includes a bump to Nextflow 25.04.8.

Full Changelog: https://github.com/nf-core/sarek/compare/3.6.0…3.6.1

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What’s Changed

Main new features

🧬 Lots of improvements around UMI support (#1937, @SPPearce) ⏩ Parabricks support (#1804, @famosab) 🔍 Muse (#1744, @famosab) and Sentieon TNScope (#1934, @SPPearce) 📜 MSISensor2 (#1965, @maxulysse) 🦖 Varlociraptor (#1940, @famosab) ◀️ Normalization of variants (#1770, @Patricie34 & @maxulysse) 🖖 bbsplit (#1983, @apsteinberg, @tobsecret & @FriederikeHanssen)

Changed

Version updates:
- VEP cache updated to v115.2
- SnpEff updated to v5.3.0a (SnpEff cache downgraded to 99 since 105 is not available at the moment)
- GATK4 to 4.6.1.0
- DeepVariant to 1.9.0
- Freebayes to 1.3.10 with QUAL filtering
Workflow improvements:
- Enhanced metro map
- Doubled default process time
- Improved sample validation
Complete test migration:
- All pytest tests migrated to nf-test framework for better testing infrastructure

Fixed

Input validation: Better samplesheet validation in #1842 by @nvnieuwk and #1858 by @kjellinjonas and bugfix addReadgroupToMeta in #1849 by @thiago-miller
CNVkit compatibility: Fixed --no_intervals usage and CPU allocation in #1928 by @SPPearce
DeepVariant configuration: Added --sample_name argument when meta.sample available in #1992 by @matthdsm

New Parameters

--freebayes_filter
--msisensor2_models
--sentieon_consensus
--umi_base_skip
--umi_in_read_header
--umi_length
--umi_location
--umi_tag
--varlociraptor_chunk_size
--varlociraptor_scenario_germline
--varlociraptor_scenario_somatic
--varlociraptor_scenario_tumor_only

Full Changelog: 3.5.1…3.6.0

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What’s Changed

Changed

Bump schema version to 2.2.1 in https://github.com/nf-core/sarek/pull/1767 by @FriederikeHanssen
Merge intervals for WES in GATK GenomicsDBImport in https://github.com/nf-core/sarek/pull/1777 by @tdanhorn

Fixed

Use file-path-pattern over file-path to hanlde glob for known_indels and known_indels_tbi to fix https://github.com/nf-core/sarek/issues/1785 in https://github.com/nf-core/sarek/pull/1797 by @maxulysse
Update GHA for full_test tests in https://github.com/nf-core/sarek/pull/1802 by @maxulysse

Full Changelog: https://github.com/nf-core/sarek/compare/3.5.0…3.5.1

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What’s Changed

New Contributors

@AitorPeseta made their first contribution in https://github.com/nf-core/sarek/pull/1620
@LouisLeNezet made their first contribution in https://github.com/nf-core/sarek/pull/1660
@nevinwu made their first contribution in https://github.com/nf-core/sarek/pull/1653
@pharmlovex made their first contribution in https://github.com/nf-core/sarek/pull/1712
@pmoris made their first contribution in https://github.com/nf-core/sarek/pull/1664
@bounlu made their first contribution in https://github.com/nf-core/sarek/pull/1624
@alexanderchang1 made their first contribution in https://github.com/nf-core/sarek/pull/1638
@lindenb made their first contribution in https://github.com/nf-core/sarek/pull/1613

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.4…3.5.0

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What’s Changed

FIX: misleading docs - xref 1621 by @maxulysse in https://github.com/nf-core/sarek/pull/1623
Correct tower snpeff by @cmatKhan in https://github.com/nf-core/sarek/pull/1627
Allow dbsnp if null in germline variant calling by @cmatKhan in https://github.com/nf-core/sarek/pull/1628

New Contributors

@cmatKhan made their first contribution in https://github.com/nf-core/sarek/pull/1627

Full Changelog: https://github.com/nf-core/sarek/compare/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 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 https://github.com/nf-core/sarek/pull/1502
Adds the cnvkit/export module, to export called CNVs into VCF by @lescai in https://github.com/nf-core/sarek/pull/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 https://github.com/nf-core/sarek/pull/1502
Simplify logic in args management by @maxulysse in https://github.com/nf-core/sarek/pull/1521
Update vep cache version to 111 by @maxulysse in https://github.com/nf-core/sarek/pull/1557
Cleanup + update modules by @maxulysse in https://github.com/nf-core/sarek/pull/1545
Updating documentation by @asp8200 in 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 https://github.com/nf-core/sarek/pull/1541
FIX: typo (strelka2 -> strelka) by @maxulysse in https://github.com/nf-core/sarek/pull/1536
FIX: Typo build_from_index -> build_only_index by @maxulysse in https://github.com/nf-core/sarek/pull/1547
FIX: Correct vep_cache_path_full when refseq/merged option is present by @YeHW in https://github.com/nf-core/sarek/pull/1563
Remove snapshot from Haplotypecaller tests by @maxulysse in https://github.com/nf-core/sarek/pull/1596
Remove snapshot from Deepvariant tests by @maxulysse in https://github.com/nf-core/sarek/pull/1597
Remove empty outdirs by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1612
Remove legacy configs of CUSTOM_DUMPSOFTWAREVERSIONS by @asp8200 in https://github.com/nf-core/sarek/pull/1542

New Contributors

@famosab made their first contribution in https://github.com/nf-core/sarek/pull/1527
@YeHW made their first contribution in https://github.com/nf-core/sarek/pull/1563

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.2…3.4.3

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What’s Changed

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

New Contributors

@kenibrewer made their first contribution in https://github.com/nf-core/sarek/pull/1501
@nh13 made their first contribution in https://github.com/nf-core/sarek/pull/1505

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

New Contributors

@sminot made their first contribution in https://github.com/nf-core/sarek/pull/1345
@mirpedrol made their first contribution in https://github.com/nf-core/sarek/pull/1365
@tdanhorn made their first contribution in https://github.com/nf-core/sarek/pull/1383
@allaway made their first contribution in https://github.com/nf-core/sarek/pull/1395
@MatthiasZepper made their first contribution in https://github.com/nf-core/sarek/pull/1420
@nschcolnicov made their first contribution in https://github.com/nf-core/sarek/pull/1400

Full Changelog: https://github.com/nf-core/sarek/compare/3.4.0…3.4.1

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What’s Changed

New tools:

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

Refactoring

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

Bug fixes and other updates

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

New Contributors

@grantn5 made their first contribution in https://github.com/nf-core/sarek/pull/1223
@RaqManzano made their first contribution in https://github.com/nf-core/sarek/pull/1286
@SPPearce made their first contribution in https://github.com/nf-core/sarek/pull/1252

Full Changelog: https://github.com/nf-core/sarek/compare/3.3.2…3.4.0

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What’s Changed

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

Full Changelog: https://github.com/nf-core/sarek/compare/3.3.1…3.3.2

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What’s Changed

FIX: Zenodo ID in manifest by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1232
FIX: Remove check annotation folders existence when no annotation by @maxulysse in https://github.com/nf-core/sarek/pull/1236
FIX: Disable JVM hotspot in gatk4 modules by @maxulysse in https://github.com/nf-core/sarek/pull/1240
UPDATE: Controlfreec version to 11.6b by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1241
FEAT: Improve schema usage for input by @maxulysse in https://github.com/nf-core/sarek/pull/1243
Simplify sentieon test license server usage by @maxulysse in https://github.com/nf-core/sarek/pull/1242

Full Changelog: https://github.com/nf-core/sarek/compare/3.3.0…3.3.1

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What’s Changed

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

New Contributors

@nicorap made their first contribution in https://github.com/nf-core/sarek/pull/1111
@rhagenson made their first contribution in https://github.com/nf-core/sarek/pull/1138
@berguner made their first contribution in https://github.com/nf-core/sarek/pull/1013
@mirpedrol made their first contribution in https://github.com/nf-core/sarek/pull/1059
@ATpoint made their first contribution in https://github.com/nf-core/sarek/pull/1166
@JohannesKersting made their first contribution in https://github.com/nf-core/sarek/pull/1192

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.3…3.3.0

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What’s Changed

FIX: Remove public_aws_ecr profile by @maxulysse in https://github.com/nf-core/sarek/pull/1118
FIX: Remove default null in schema by @maxulysse in https://github.com/nf-core/sarek/pull/1119
CHORES: Prepare 3.2.3 by @asp8200 in https://github.com/nf-core/sarek/pull/1128
Release candidate 3.2.3 by @asp8200 in https://github.com/nf-core/sarek/pull/1129

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.2…3.2.3

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What’s Changed

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

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.1…3.2.2

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What’s Changed

CHORES: back to dev by @maxulysse in https://github.com/nf-core/sarek/pull/1073
fix typo in profile name by @maxulysse in https://github.com/nf-core/sarek/pull/1079
FIX: update bgziptabix module by @maxulysse in https://github.com/nf-core/sarek/pull/1078
CHORES: Prepare release 3.2.1 by @maxulysse in https://github.com/nf-core/sarek/pull/1080
FIX: patch more modules by @maxulysse in https://github.com/nf-core/sarek/pull/1082
Release candidate 3.2.1 by @maxulysse in https://github.com/nf-core/sarek/pull/1081

Full Changelog: https://github.com/nf-core/sarek/compare/3.2.0…3.2.1

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What’s Changed

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

New Contributors

@robsyme made their first contribution in https://github.com/nf-core/sarek/pull/971
@matrulda made their first contribution in https://github.com/nf-core/sarek/pull/978
@ameynert made their first contribution in https://github.com/nf-core/sarek/pull/981
@adamrtalbot made their first contribution in https://github.com/nf-core/sarek/pull/1031
@amizeranschi made their first contribution in https://github.com/nf-core/sarek/pull/1050

Full Changelog: https://github.com/nf-core/sarek/compare/3.1.2…3.2.0

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What’s Changed

Release 3.1.2 by @maxulysse in https://github.com/nf-core/sarek/pull/906

Full Changelog: https://github.com/nf-core/sarek/compare/3.1.1…3.1.2

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What’s Changed

Syn up dev by @maxulysse in https://github.com/nf-core/sarek/pull/849
Remove “None” definition from schema by @drpatelh in https://github.com/nf-core/sarek/pull/851
Md cram update by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/855
Add R64-1-1 and UMD3.1 by @maxulysse in https://github.com/nf-core/sarek/pull/856
prepare release 3.1.1 by @maxulysse in https://github.com/nf-core/sarek/pull/858
release 3.1.1 by @maxulysse in https://github.com/nf-core/sarek/pull/857

Full Changelog: https://github.com/nf-core/sarek/compare/3.1…3.1.1

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What’s Changed

Back to business on dev by @maxulysse in https://github.com/nf-core/sarek/pull/762
Update subway map by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/766
Dev deepvariant by @maxulysse in https://github.com/nf-core/sarek/pull/768
Fix gatk4 cnnscorevariants by @maxulysse in https://github.com/nf-core/sarek/pull/770
add logo for Danish National Genome Center by @maxulysse in https://github.com/nf-core/sarek/pull/774
update to new modules syntax + patch on non-up to date modules by @maxulysse in https://github.com/nf-core/sarek/pull/771
nf core template merge 2.6 by @maxulysse in https://github.com/nf-core/sarek/pull/773
AWS outdir paths were mixed up by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/777
Add this years posters by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/775
use chr length file by default since cf is otherwise not working by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/783
No scatter on full size tests to avoid issues with in or output files randomly not staged by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/782
Updated docs of bcftools stats variant depth by @SusiJo in https://github.com/nf-core/sarek/pull/788
ci: Move tmpdir to ~ by @Emiller88 in https://github.com/nf-core/sarek/pull/791
Fix somatic test with mutect2 by @SusiJo in https://github.com/nf-core/sarek/pull/790
Md cram by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/735
don’t annotate gvcfs by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/793
Don’t publish unzip files by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/794
Update ci.yml by @maxulysse in https://github.com/nf-core/sarek/pull/796
Update all subworkflows name by @maxulysse in https://github.com/nf-core/sarek/pull/784
Fix sample header error when starting from bams by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/807
More complete CI by @maxulysse in https://github.com/nf-core/sarek/pull/806
add rgid, to separate sample info by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/814
Fix validation of input when launching from website by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/813
collect cnvkit reference to not be consumed by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/817
prioritze test conf for mutect in tests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/815
Use putIfAbsent by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/821
add speed up parameters for genomicsdb by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/827
Add option for cnvkit to provide external Cnn reference by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/825
add more docs about scatter/gather by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/820
Fix bug with no variantcalling when starting from step recalibration Issue 763 by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/828
Update modules & tool versions by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/822
Get ride of copyTo to enable s3 buckets in different regiosn by @maxulysse in https://github.com/nf-core/sarek/pull/839
remove cf len file from config by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/841
increase samtools stats memory by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/842

Full Changelog: https://github.com/nf-core/sarek/compare/3.0.2…3.1

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What’s Changed

Fix Vep plugin usage by @BarryDigby in https://github.com/nf-core/sarek/pull/688
Fix when clause for building mapping indexes by @maxulysse in https://github.com/nf-core/sarek/pull/689
Updating nf-core-modules by @asp8200 in https://github.com/nf-core/sarek/pull/685, https://github.com/nf-core/sarek/pull/734
Fix schema for controlfreec ploidy by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/704
Vep Issues: loftee needs version by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/706
Adding md5-sums to the test-yml-files by @asp8200 in https://github.com/nf-core/sarek/pull/696
sync 2.5 by @maxulysse in https://github.com/nf-core/sarek/pull/720
Dev sync 2.5.1 by @maxulysse in https://github.com/nf-core/sarek/pull/723
Subway update by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/719
Add in Azure config documentation by @vsmalladi in https://github.com/nf-core/sarek/pull/716
Add further support ControlFreec for targeted data by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/728
Allow interval.{bed,interval,interval_list} files by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/727
Switch germline and somatic full tests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/731
Optimize resource requests by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/726
Add testing for conda/singularity by @maxulysse in https://github.com/nf-core/sarek/pull/736, https://github.com/nf-core/sarek/pull/691
Clean up publishing by @FriederikeHanssen and @maxulysse in https://github.com/nf-core/sarek/pull/741, https://github.com/nf-core/sarek/pull/705, https://github.com/nf-core/sarek/pull/681
Additional input checks by @asp8200 in https://github.com/nf-core/sarek/pull/742
Test profiles separated into multiple files to support usage with tower by @maxulysse in https://github.com/nf-core/sarek/pull/743, https://github.com/nf-core/sarek/pull/692
Remove errorStrategy in modules.config by @drpatelh in https://github.com/nf-core/sarek/pull/757
update zenodo link to point to latest by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/758

New Contributors

@BarryDigby made their first contribution in https://github.com/nf-core/sarek/pull/688
@vsmalladi made their first contribution in https://github.com/nf-core/sarek/pull/715
@drpatelh made their first contribution in https://github.com/nf-core/sarek/pull/757

Full Changelog: https://github.com/nf-core/sarek/compare/3.0.1…3.0.2

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What’s Changed

Fix usage of intervals in samtools/mpileup by @nickhsmith in https://github.com/nf-core/sarek/pull/708

Full Changelog: https://github.com/nf-core/sarek/compare/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 https://github.com/nf-core/sarek/pull/394
@nickhsmith made their first contribution in https://github.com/nf-core/sarek/pull/454
@Emiller88 made their first contribution in https://github.com/nf-core/sarek/pull/465
@priesgo made their first contribution in https://github.com/nf-core/sarek/pull/432
@SusiJo made their first contribution in https://github.com/nf-core/sarek/pull/545
@asp8200 made their first contribution in https://github.com/nf-core/sarek/pull/571
@lassefolkersen made their first contribution in https://github.com/nf-core/sarek/pull/591
@WackerO made their first contribution in https://github.com/nf-core/sarek/pull/570

Full Changelog: https://github.com/nf-core/sarek/compare/2.7.2…3.0

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What’s Changed

Fix MapReads caching bug by @BrunoGrandePhD in https://github.com/nf-core/sarek/pull/566

Full Changelog: https://github.com/nf-core/sarek/compare/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