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