nf-core/rnaseq v3.26.0 - Chromium Cuttlefish

What's Changed

• Bump version after release 3.25.0 by @pinin4fjords in #1821
• Patch release 3.25.1: trimgalore same-workdir-retry cleanup by @pinin4fjords in #1823
• docs(changelog): restore #1821 entry under 3.25.1 by @pinin4fjords in #1824
• Disambiguate FastQC General Stats columns; revert 3.25.1 release bump by @pinin4fjords in #1829
• bump(trimgalore): module to 2.1.0 (TrimGalore v2 Oxidized Edition GA) by @FelixKrueger in #1789
• Important! Template update for nf-core/tools v4.0.2 by @nf-core-bot in #1827
• Important! Template update for nf-core/tools v4.0.0 by @nf-core-bot in #1826
• Suppress non-comparable lengthScaledTPM gene-count files in --skip_quantification_merge mode by @pinin4fjords in #1832
• fix(tximport): publish augmented tx2gene actually used by tximport by @pinin4fjords in #1831
• feat(star): gate legacy STAR pin on per-entry star_legacy flag by @pinin4fjords in #1834
• Drop legacy STAR 2.6.1d pin; upgrade iGenomes index params instead by @pinin4fjords in #1835
• Reinstall trimgalore + add process_low_memory label to base.config by @pinin4fjords in #1836
• Bump version to 3.26.0 ahead of release by @pinin4fjords in #1837
• Address review feedback from #1838 by @pinin4fjords in #1839
• Address review feedback from #1838 (Vag) by @pinin4fjords in #1840
• fix(trimgalore): restore --cores 8 by pinning TRIMGALORE to 12 cpus by @pinin4fjords in #1841
• fix(trimgalore): drop TRIMGALORE override from 12 to 8 cpus by @pinin4fjords in #1842
• Dev -> master for nf-core/rnaseq 3.26.0 by @pinin4fjords in #1838

New Contributors

• @FelixKrueger made their first contribution in #1789

Full Changelog: 3.25.0...3.26.0

nf-core/rnaseq v3.25.0 - Plutonium Pangolin

What's Changed

• Bump version to 3.25.0dev; fix SortMeRNA sample name in MultiQC by @pinin4fjords in #1781
• refactor: delocalise GTF_FILTER to nf-core custom/gtffilter by @pinin4fjords in #1782
• fix: wire up skip_gtf_transcript_filter to CUSTOM_GTFFILTER ext.args by @pinin4fjords in #1783
• Replace local gtf2bed with nf-core ea-utils/gtf2bed module by @pinin4fjords in #1784
• refactor: replace local BAM QC with nf-core bam_qc_rnaseq subworkflow by @pinin4fjords in #1786
• feat: add GPU support for ribodetector by @pinin4fjords in #1790
• refactor: centralize module configs in conf/modules/ by @pinin4fjords in #1788
• Bump custom/multiqccustombiotype to fail loudly on high biotype cardinality by @pinin4fjords in #1795
• feat: add strand-agnostic bigwig, skip per-strand for unstranded libraries by @pinin4fjords in #1792
• Fix MultiQC collapsing _1/_2 sample IDs via per-sample lookbehind by @pinin4fjords in #1793
• docs: clarify prokaryotic transcript extraction includes tRNA/rRNA/tmRNA/ncRNA by @pinin4fjords in #1796
• Add stringtie_merge for de novo assembly by @Odulhin in #1755
• fix(prokaryotic): skip StringTie by default in the prokaryotic profile by @pinin4fjords in #1804
• fix: per-sample MultiQC progressive closure via structural .join chain by @pinin4fjords in #1803
• feat(bowtie2_salmon): report up to -k 200 alignments so Salmon EM can work by @pinin4fjords in #1806
• fix(sortmerna): adopt SortMeRNA SILVA 138 smr_v4.3_default_db as the default rRNA database by @pinin4fjords in #1811
• fix(mqc): strandedness table rows reflect which analyses ran; narrow prokaryotic RSeQC skip by @pinin4fjords in #1805
• test: dedupe pipeline-level tests without losing coverage by @pinin4fjords in #1812
• chore: sync nf-core components and retire ch_versions plumbing by @pinin4fjords in #1814
• test(cleanup): gate pipeline-test cleanup on CI to keep local reruns stable by @pinin4fjords in #1815
• Bump version to 3.25.0 ahead of release by @pinin4fjords in #1799
• fix(prokaryotic): derive gene BED via gffread --bed by @pinin4fjords in #1817
• chore: drop redundant versions.yml filters from saveAs closures by @pinin4fjords in #1818
• fix(prokaryotic): skip RSeQC infer_experiment on bowtie2_salmon + skip sentieon on conda by @pinin4fjords in #1819
• Dev -> master for nf-core/rnaseq 3.25.0 by @pinin4fjords in #1816

New Contributors

• @Odulhin made their first contribution in #1755

Full Changelog: 3.24.0...3.25.0

nf-core/rnaseq v3.24.0 - Selenium Seahorse

What's Changed

• fix: always set ID/SM read group tags; bump version to 3.24.0dev by @pinin4fjords in #1740
• fix: always skip igenomes_base validation by @pinin4fjords in #1745
• fix: update bowtie2 modules to fix version extraction with Perl locale warnings by @pinin4fjords in #1749
• docs: add missing tool citations to CITATIONS.md by @pinin4fjords in #1750
• feat: add --skip_quantification_merge for per-sample tximport by @pinin4fjords in #1744
• docs: clarify GFF files must use --gff parameter by @pinin4fjords in #1751
• Add evaluation of trimmed data and aligners kranken - check contamination before aligners - enhancement by @EladH1 in #1746
• Fix iGenomes STAR version detection and index building logic by @pinin4fjords in #1756
• fix: remove STAR from RSEM conda environments for ARM compatibility by @pinin4fjords in #1752
• fix: restore extra_star_align_args dedup to prevent STAR duplicate parameter error by @pinin4fjords in #1762
• fix: distinguish Bowtie2 alignment from rRNA removal in MultiQC report by @pinin4fjords in #1761
• Add RustQC as optional single-pass QC replacement by @pinin4fjords in #1754
• chore: Update nf-core template to v3.5.2 by @pinin4fjords in #1764
• Bump version to 3.24.0 ahead of release by @pinin4fjords in #1763
• Update samtools modules to 1.23.1 by @pinin4fjords in #1766
• Remove --star from RSEM preparereference test config by @pinin4fjords in #1769
• Exclude non-deterministic qualimap multiqc files from snapshots by @pinin4fjords in #1770
• Update actions/upload-artifact from v3 to v7 in cloud test workflows by @pinin4fjords in #1768
• Update ribodetector module to 0.3.3 by @pinin4fjords in #1771
• Update ribodetector ARM64 container to 0.3.3 by @pinin4fjords in #1772
• Fix megatest debug log upload on launch failure by @pinin4fjords in #1774
• Update RustQC to 0.2.1 by @pinin4fjords in #1779
• docs: clarify test profile requirement for local nf-test runs by @pinin4fjords in #1778
• Dev -> master for nf-core/rnaseq 3.24.0 by @pinin4fjords in #1765

Full Changelog: 3.23.0...3.24.0

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