nf-core/sarek: 3.5.0 - Áhkájiegna

What's Changed

Added

• Tool: Lofreq callparallel by @AitorPeseta and @nevinwu in https://github.com/nf-core/sarek/pull/1620, https://github.com/nf-core/sarek/pull/1653, https://github.com/nf-core/sarek/pull/1752
• Tool: Indexcov by @lindenb in https://github.com/nf-core/sarek/pull/1613, https://github.com/nf-core/sarek/pull/1752
• Expose fastp parameter --length_required by @LouisLeNezet in https://github.com/nf-core/sarek/pull/1660
• Variant Calling tutorial pages to Usage section by @lescai in https://github.com/nf-core/sarek/pull/1706
• Pipeline level tests by @maxulysse in https://github.com/nf-core/sarek/pull/1661,https://github.com/nf-core/sarek/pull/1669
• Check if flowcell id matches for paired samples by @pmoris in https://github.com/nf-core/sarek/pull/1664
• Documentation on how to use WES ASCAT with chr prefixed bed file by @alexanderchang1 in https://github.com/nf-core/sarek/pull/1638

Changed

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

Fixed

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

Removed

• Retire snpeff_genome by @asp8200 in https://github.com/nf-core/sarek/pull/1656
• Remove Strelka tumor-only somatic variant calling by @nevinwu in https://github.com/nf-core/sarek/pull/1709
• Remove defaults channel from nf-core conda environments by @maxulysse in https://github.com/nf-core/sarek/pull/1663
• Remove defaults channel from local modules by @FriederikeHanssen in https://github.com/nf-core/sarek/pull/1755

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