Sarek 3.4.1 - Balgattjåhkkå

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