nf-core/rnaseq v3.23.0 - Gallium Gecko

What's Changed

• Bump version after release 3.22.2 by @pinin4fjords in #1663
• Update preprocessing with multiple rRNA removal tools by @pinin4fjords in #1664
• Add ARM containers, changelog updates, and bulk module/subworkflow updates by @pinin4fjords in #1665
• New module for contamination screening: Sylph by @egreenberg7 in #1616
• Enable SeqKit stats MultiQC module for RiboDetector rRNA removal by @pinin4fjords in #1669
• fix: Enhance RSEM output exports and remove unnecessary star_rsem check by @EladH1 in #1667
• Document star_rsem STAR aligner settings and customization by @cmatKhan in #1672
• Apply Nextflow 25 strict syntax fixes by @pinin4fjords in #1677
• fix(tests): Comprehensive PREPARE_GENOME test fixes for proper aligner coverage by @pinin4fjords in #1687
• feat: Migrate to topic-based version reporting by @pinin4fjords in #1689
• feat: Add prokaryotic RNA-seq support with -profile prokaryotic by @pinin4fjords in #1688
• feat: Add support for uncompressed FASTQ input files by @pinin4fjords in #1686
• Fix offline mode by skipping igenomes_base validation by @pinin4fjords in #1696
• refactor: Replace local iGenomes STAR modules with nf-core aliases by @pinin4fjords in #1694
• Add GPU accelerated STAR and Markdups (using Parabricks rna_fq2bam) by @gburnett-nvidia in #1685
• Add FastQC step after BBSplit/rRNA filtering by @pinin4fjords in #1700
• fix: Include single-library samples in merged fastq output by @pinin4fjords in #1704
• feat: Add tximport processing for RSEM outputs (#1320) by @pinin4fjords in #1697
• feat: Enable UMI deduplication with STAR/RSEM aligner by @pinin4fjords in #1707
• fix: Allow pre-built pseudo-aligner index without --fasta by @pinin4fjords in #1708
• docs: update metro map renders with nf-metro v0.4.7 by @pinin4fjords in #1709
• Fix GPU profile applying container flags globally by @pinin4fjords in #1711
• refactor: seq_platform/seq_center via ext.args closures by @pinin4fjords in #1713
• Bump version to 3.23.0 ahead of release by @pinin4fjords in #1715
• Fix: informative error when Salmon strandedness inference fails by @pinin4fjords in #1716
• Add --seq_platform parameter for global sequencing platform RG tag by @pinin4fjords in #1718
• Docs and changelog cleanup by @pinin4fjords in #1719
• Update umitools modules: remove patches, add channel prefixes by @pinin4fjords in #1724
• Refine .nftignore patterns and update test snapshots by @pinin4fjords in #1725
• docs: regenerate metro map with nf-metro v0.5.1 by @pinin4fjords in #1714
• docs: re-render metro map with nf-metro v0.5.4 by @pinin4fjords in #1728
• ci: bump Nextflow to 25.04.3 to fix conda --mkdir bug by @pinin4fjords in #1730
• refactor: code quality improvements from PR #1717 review by @pinin4fjords in #1735
• refactor: compose test_prokaryotic profile on prokaryotic by @pinin4fjords in #1734
• test: load prokaryotic config in nf-test instead of duplicating params by @pinin4fjords in #1736
• Fix iGenomes STAR conda channel for x86_64 by @pinin4fjords in #1738
• Dev -> master for nf-core/rnaseq 3.23.0 by @pinin4fjords in #1717

New Contributors

• @cmatKhan made their first contribution in #1672
• @gburnett-nvidia made their first contribution in #1685

Full Changelog: 3.22.2...3.23.0

nf-core/rnaseq v3.22.2 - Perfect Palladium Penguin

What's Changed

• Bump after release 3.22.1 by @pinin4fjords in #1656
• Bump nf-core/multiqc module by @pinin4fjords in #1658
• Update MultiQC ARM container to 1.33 by @pinin4fjords in #1660
• Fix duplicate flagstat files in MultiQC report by @pinin4fjords in #1655
• fix(tximport): handle tx2gene files with extra columns by @pinin4fjords in #1654
• Reduce duplicate coverage in pipeline tests by @pinin4fjords in #1648
• Fix MultiQC sample name collisions with shared FASTQ filenames by @pinin4fjords in #1659
• Bump version to 3.22.2 ahead of release by @pinin4fjords in #1661
• Dev -> master for nf-core/rnaseq 3.22.2 by @pinin4fjords in #1662

Full Changelog: 3.22.1...3.22.2

nf-core/rnaseq v3.22.1 - Polished Palladium Penguin

What's Changed

• Bump after release 3.22.0 by @pinin4fjords in #1640
• add ARM CI test by @mashehu in #1641
• Long merge rsem by @EladH1 in #1642
• Fix HISAT2 issues: BAM CSI index with UMI deduplication by @pinin4fjords in #1645
• Bump version to 3.22.1 ahead of release by @pinin4fjords in #1647
• Restrict ARM CI tests to Docker profile only by @pinin4fjords in #1650
• Add dupMatrix files to nftignore for reproducibility by @pinin4fjords in #1651
• Dev -> master for nf-core/rnaseq 3.22.1 by @pinin4fjords in #1649

Full Changelog: 3.22.0...3.22.1

nf-core/rnaseq v3.22.0 - Palladium Penguin

What's Changed

• Bump after release 3.21.0 by @pinin4fjords in #1608
• Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in #1614
• Bbsplit staging issue by @EladH1 in #1617
• Optimize qualimap performance with multi-threaded name sorting by @pinin4fjords in #1621
• Fix bigwig strand labeling for reverse-stranded libraries by @pinin4fjords in #1620
• Fix CI: Ensure confirm-pass job runs for markdown-only PRs by @pinin4fjords in #1618
• usage - fix broken link and add latest kit version for Takara UMI prep by @pontushojer in #1613
• Update tximeta/tximport module to fix sample name mangling by @pinin4fjords in #1623
• Important! Template update for nf-core/tools v3.5.1 by @nf-core-bot in #1628
• Document Qualimap read counting limitation by @pinin4fjords in #1625
• Document RSeQC inner_distance limitation for large chromosomes by @pinin4fjords in #1624
• Update Credits to reflect current maintainership by @pinin4fjords in #1619
• Fix bbsplit index staging by using symlinks by @pinin4fjords in #1631
• Fix arm64 profile configuration by @pinin4fjords in #1630
• Add validation error for incompatible transcript_fasta and additional_fasta params by @Copilot in #1633
• Add validation error for incompatible transcript_fasta and additional_fasta params by @Copilot in #1634
• Fix --gtf_extra_attributes to support multiple comma-separated values by @pinin4fjords in #1635
• Simplify workflow nextflow.config by consolidating redundant patterns by @pinin4fjords in #1636
• Add validation error for incompatible transcript_fasta and additional_fasta params by @pinin4fjords in #1632
• Bump version to 3.22.0 ahead of release by @pinin4fjords in #1638
• Dev -> master for nf-core/rnaseq 3.22.0 by @pinin4fjords in #1639

New Contributors

• @EladH1 made their first contribution in #1617
• @pontushojer made their first contribution in #1613
• @Copilot made their first contribution in #1633

Full Changelog: 3.21.0...3.22.0

nf-core/rnaseq v3.21.0 - Mercury Macaw

What's Changed

• Bump version back to dev after release 3.20.0 by @maxulysse in #1597
• Add bam input pathway by @pinin4fjords in #1603
• Enable BAM input for RSEM by @pinin4fjords in #1604
• Fix default for umi_discard_read to prevent validation errors in Platform by @pinin4fjords in #1605
• Bump version to 3.21.0 ahead of release by @pinin4fjords in #1606
• Dev -> Master for 3.21.0 by @pinin4fjords in #1607

Full Changelog: 3.20.0...3.21.0

nf-core/rnaseq v3.20.0 - Iridium Impala

What's Changed

• back to dev + nft-utils 0.0.4 by @maxulysse in #1568
• Update awsfulltest.yml to restore aligner-wise output by @pinin4fjords in #1585
• Important! Template update for nf-core/tools v3.3.2 by @nf-core-bot in #1580
• [GH-1572] Fix salmon.merged.SummarizedExperiment.rds name collision by @GallVp in #1573
• For umitools use only umi_dedup.sorted.log in multiqc_report by @idot in #1571
• Add sentieon star by @FriederikeHanssen in #1590
• Bump version to 3.20.0 ahead of release by @FriederikeHanssen in #1592
• Exclude star rsem pca from snaps by @pinin4fjords in #1594
• Exclude unstable star_rsem clusterings from snaps by @pinin4fjords in #1595
• Dev -> Master for 3.20.0 by @pinin4fjords in #1593

New Contributors

• @GallVp made their first contribution in #1573
• @idot made their first contribution in #1571

Full Changelog: 3.19.0...3.20.0

nf-core/rnaseq v3.19.0 - Tungsten Turtle

What's Changed

• Bump versions after release 3.18.0 by @pinin4fjords in #1480
• Update trimgalore module for save_unpaired fix by @pinin4fjords in #1482
• Bump STAR build for multiprocessing fix by @pinin4fjords in #1486
• Make genomic FASTA input optional by @pinin4fjords in #1490
• fix rendering of DE tutorial by @mashehu in #1493
• Bump MultiQC module to 1.27 by @pinin4fjords in #1499
• Important! Template update for nf-core/tools v3.2.0 by @nf-core-bot in #1496
• Fix missing Bracken results in the MultiQC report by @davidecarlson in #1508
• Update README.md by @AlenaNik in #1518
• updated the conda package version specification for Perl for the local module gtf2bed by @delagoya in #1521
• Update preprocessing subworkflow to fix linting block on trimming by @pinin4fjords in #1523
• Json schema improvements by @glichtenstein in #1528
• Make jobs automatically resubmit for exit code 175 by @fntlnz in #1553
• Unify summarised experiment by @atrigila in #1550
• Update index docs to remove references to 'indexing only mode' by @pinin4fjords in #1556
• Remove patches and bump modules for ARM compat by @pinin4fjords in #1558
• Important! Template update for nf-core/tools v3.3.1 by @nf-core-bot in #1559
• General modules update, include updating subworkflows for stats fixes by @pinin4fjords in #1560
• Version bumps ahead of 3.19.0 release by @pinin4fjords in #1563
• Improve reproducibility with Conda by @pinin4fjords in #1565
• Prerelease 3.19.0 fixes by @pinin4fjords in #1567
• Dev -> Master for 3.19.0 by @pinin4fjords in #1564

New Contributors

• @davidecarlson made their first contribution in #1508
• @AlenaNik made their first contribution in #1518
• @delagoya made their first contribution in #1521
• @glichtenstein made their first contribution in #1528
• @fntlnz made their first contribution in #1553
• @atrigila made their first contribution in #1550

Full Changelog: 3.18.0...3.19.0

nf-core/rnaseq v3.18.0 - Lithium Lynx

What's Changed

• Adding differential expression analysis tutorial pages to Usage section by @LorenzoS96 in #1447
• Add FASTQ linting during preprocessing by @pinin4fjords in #1461
• Add umicollapse as an alternative to umi-tools by @siddharthab in #1369
• Move channel operations outside of the onComplete() block by @robsyme in #1463
• Add test suite for UMI handling functionality by @pinin4fjords in #1467
• Factor out umi handling by @pinin4fjords in #1466
• Remove reference to unused "skip_sample_count" value in email templates by @robsyme in #1459
• Minor docs fix by @pinin4fjords in #1469
• Update subworkflow to account for fix to bad argument handling by @pinin4fjords in #1470
• Fix prepare_genome subworkflow for sortmerna by @pinin4fjords in #1471
• Bump STAR modules by @pinin4fjords in #1473
• Bump versions to 3.18.0 by @pinin4fjords in #1474
• Fix log publishing around umitools/ umicollapse by @pinin4fjords in #1475
• Update from master by @pinin4fjords in #1477
• Update CHANGELOG.md by @pinin4fjords in #1479
• Dev -> Master for 3.18.0 by @pinin4fjords in #1476

New Contributors

• @LorenzoS96 made their first contribution in #1447
• @siddharthab made their first contribution in #1369

Full Changelog: 3.17.0...3.18.0

nf-core/rnaseq v3.17.0 - Neon Newt

This is a minor release done to improve ARM compatibility in the pipeline.

What's Changed

• Update dev from master by @pinin4fjords in #1417
• Bump versions back to 3.17.0 after release by @pinin4fjords in #1418
• Bump lots of modules so that conda versions have arm builds by @pinin4fjords in #1422
• Bump STAR version for version with ARM Conda build by @pinin4fjords in #1423
• patch sortmerna to 4.3.7 for ARM compatibility by @pinin4fjords in #1424
• Backport support for Graviton 4 to version 3.16.1 by @pabloaledo in #1414
• Add profile for ARM compatibility by @pinin4fjords in #1425
• Bump versions for 3.17.0 release by @pinin4fjords in #1432
• No exception for default registry by @maxulysse in #1434
• update CHANGELOG by @maxulysse in #1437
• Reduce matrix by @maxulysse in #1440
• Fix nf-core download test by @maxulysse in #1441
• Dev -> Master for 3.17.0 by @pinin4fjords in #1433

New Contributors

• @pabloaledo made their first contribution in #1414

Full Changelog: 3.16.1...3.17.0

nf-core/rnaseq v3.16.1 - Further Fire Ferret

What's Changed

• Back to dev by @maxulysse in #1398
• Important! Template update for nf-core/tools v3.0.1 by @nf-core-bot in #1401
• Important! Template update for nf-core/tools v3.0.2 by @nf-core-bot in #1407
• Fix bad variable name in subworkflow by @pinin4fjords in #1405
• FIX: Keep only one samplesheetToList by @maxulysse in #1406
• Fix issues caused by empty versions from trimming subworkflows by @pinin4fjords in #1410
• Fix manifest text by @maxulysse in #1409
• Reset versions back to 3.16.1 for patch release by @pinin4fjords in #1412
• FIX: Disable pipeline level conda tests by @maxulysse in #1415
• Properly disable conda pipeline level tests by @maxulysse in #1416
• Dev -> Master for 3.16.1 by @pinin4fjords in #1413

Full Changelog: 3.16.0...3.16.1