Release Sarek 3.5.0 - Áhkájiegna · nf-core/sarek

What's Changed

Tool: Lofreq callparallel by @AitorPeseta and @nevinwu in #1620, #1653, #1752
Tool: Indexcov by @lindenb in #1613, #1752
Expose fastp parameter --length_required by @LouisLeNezet in #1660
Variant Calling tutorial pages to Usage section by @lescai in #1706
Pipeline level tests by @maxulysse in #1661
Check if flowcell id matches for paired samples by @pmoris in #1664
Documentation on how to use WES ASCAT with chr prefixed bed file by @alexanderchang1 in #1638

Template update for nf-core/tools v3.0.0, v3.0.1, v3.0.2 by @nf-core-bot in #1680, #1681, #1686
Update CI actions by @maxulysse in #1657
Migrate to nf-test by @maxulysse in #1678, #1708, #1731, #1711
Add nf-test sharding CI by @edmundmiller in #1668
style: Enable harshilAlignment in VS Code workspace by @edmundmiller in #1730
Print warnings if flowcell ID cannot be retrieved instead of erroring for Nextflow <24.08.0-edge by @maxulysse in #1673
Clean up schema file and unhid almost all parameters by @FriederikeHanssen in #1707
Don't convert input bam files that are supplied in post-alignment steps by @FriederikeHanssen in #1728
Update all modules by @maxulysse in #1695, #1692, #1663

Fix: template_version_comment GHA by @mirpedrol in #1684
Fix: flowcell access by @FriederikeHanssen in #1693
Fix: manifest DOI display on CLI by @maxulysse in #1694
Fix: nf-schema tests that were not failing on lenient mode by @maxulysse in #1702
Fix: Missing import statements on error messages(#1566) by @pharmlovex in #1712
Fix: Convert bcf_annotations.tbi from empty() to value channel to prevent stalling by @bounlu in #1624
Fix: Add missing spring and ubam files to overview pictures by @FriederikeHanssen in #1734
Fix: add setup java 17 by @maxulysse in #1743
Fix: bug where workflow can hang if the email parameter is set. by @robsyme in #1745
Fix: Sentieon and add docs by @FriederikeHanssen and @edmundmiller in #1746, #1579
Fix: Update variant calling tool - data type table in docs by @famosab in #1635
Fix: test string by @FriederikeHanssen in #1754

Retire snpeff_genome by @asp8200 in #1656
Remove Strelka tumor-only somatic variant calling by @nevinwu in #1709
Remove defaults channel from nf-core conda environments by @maxulysse in #1663
Remove defaults channel from local modules by @FriederikeHanssen in #1755

Full Changelog: 3.4.4...3.5.0