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

nf-core/rnaseq v3.16.0 - Fire Ferret

What's Changed

• nf-core pipelines bump-version 3.16.0dev by @maxulysse in #1386
• New module: Kraken2/Bracken on Unaligned Sequences for Contamination Detection by @egreenberg7 in #1388
• Fix invalid named parameter syntax by @pditommaso in #1376
• update animated subway map by @maxulysse in #1389
• patch bedtools/genomecov to use quay.io to solve issue with nf-core download by @maxulysse in #1393
• Improve pipeline level snapshots by @maxulysse in #1379
• prepare RC 3.16.0 by @maxulysse in #1394
• RC 3.16.0 by @maxulysse in #1395

New Contributors

• @egreenberg7 made their first contribution in #1388

Full Changelog: 3.15.1...3.16.0

nf-core/rnaseq v3.15.1 - Augmented Aluminium Axolotl

What's Changed

• Bump pipeline version to 3.16.0dev by @pinin4fjords in #1374
• Fix issues with R modules changing sample names by @pinin4fjords in #1380
• Massive conda modules update by @maxulysse in #1381
• Slight fixes for rnaseq preprocessing by @pinin4fjords in #1382
• Prerelease 3.15.1 version bumps by @pinin4fjords in #1383
• Master merge by @pinin4fjords in #1385
• Dev -> Master for 3.15.1 by @pinin4fjords in #1384

Full Changelog: 3.15.0...3.15.1

nf-core/rnaseq v3.15.0 - Aluminium Axolotl

What's Changed

• Bump pipeline version to 3.15.0dev by @drpatelh in #1180
• update qualimap/rnaseq by @maxulysse in #1186
• Delete lib directory and replace with utils_* subworkflows by @drpatelh in #1197
• Replace modules.config with more modular config files per module/subworkflow/workflow by @drpatelh in #1199
• Important! Template update for nf-core/tools v2.12 by @nf-core-bot in #1201
• Remove lib directory and modules.config by @drpatelh in #1206
• CHORES: Update all modules by @maxulysse in #1212
• Use pseudoalignment subworkflow components from nf-core/modules by @pinin4fjords in #1210
• Pass transcriptome fasta through to samtools stats by @pinin4fjords in #1213
• Bump umitools + delocalise prepareforrsem by @pinin4fjords in #1214
• Delocalise catadditionalfasta by @pinin4fjords in #1216
• chore: Emiller88 => edmundmiller by @edmundmiller in #1217
• Important! Template update for nf-core/tools v2.13 by @nf-core-bot in #1218
• nf-test at the pipeline level by @adamrtalbot in #1220
• Reuse bbsplit index and don't keep overwriting by @pinin4fjords in #1226
• Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in #1229
• Add all nf-core modules and CI/CD and all nf-tests to everything by @adamrtalbot in #1221
• Update sortmerna usage by @maxulysse in #1231
• Adding tests for star_genomegenerate_igenomes by @maxulysse in #1232
• Switch to genomecov from nf-core by @pinin4fjords in #1234
• Add nf-test to local module GTF_FILTER by @adamrtalbot in #1236
• nf-test: utils_nfcore_rnaseq_pipeline tests by @adamrtalbot in #1235
• add nf-tests for star_align_igenomes by @maxulysse in #1233
• nf-test for PREPROCESS_TRANSCRIPTS_FASTA_GENCODE by @adamrtalbot in #1238
• Fix concurrency error in Github CI workflow by @adamrtalbot in #1237
• ALIGN_STAR - add nf-test tests by @maxulysse in #1239
• Swtich to dupradar from nf-core by @pinin4fjords in #1242
• Add nf-tests for deseq2_qc local module by @adamrtalbot in #1241
• Fix genomes params usage by @maxulysse in #1240
• Add gtf2bed tests by @pinin4fjords in #1244
• nf test quantify rsem by @adamrtalbot in #1245
• nf-test for module MULTIQC_CUSTOM_BIOTYPE by @adamrtalbot in #1243
• nf-test prepare_genome by @maxulysse in #1247
• Replace deseq2qc paths by @adamrtalbot in #1251
• Make README usage consistent with docs/usage.md by @pinin4fjords in #1228
• Remove all tags.yml files by @adamrtalbot in #1250
• Include nf-tests for rsem_merge_counts module by @robsyme in #1249
• nf-test quantify pseudoalignment by @adamrtalbot in #1246
• Update CHANGELOG by @drpatelh in #1260
• Try to fix CI pipeline AGAIN by @adamrtalbot in #1262
• Small updates noticed during code review by @drpatelh in #1265
• Delete unecessary tags from nf.test files for modules and subworkflows by @drpatelh in #1266
• Add more tests for PREPARE_GENOME by @adamrtalbot in #1261
• Fixup: Add GHA files back into include statement of Github workflow change detection by @adamrtalbot in #1264
• Update trimming subworkflow to include more tests by @adamrtalbot in #1271
• Delocalise pseudo quant workflow by @pinin4fjords in #1278
• Update bam_markduplicates_picard subworkflow by @adamrtalbot in #1274
• Simple pipeline level nf-tests by @adamrtalbot in #1272
• Add new testing strategy based on nf-test files by @adamrtalbot in #1253
• Add psueudoaligner pipeline level tests to test suite by @adamrtalbot in #1279
• Reorganise pipeline tests into flat structure by @adamrtalbot in #1280
• Fix CHANGELOG error by @adamrtalbot in #1282
• Increase contents of default.main.nf.test.snap by @adamrtalbot in #1283
• Improved ext.args consolidation for STAR and TRIMGALORE by @MatthiasZepper in #1248
• Fix genomeAttribute usage by @maxulysse in #1252
• fix(subworkflow): update utils_nfcore_pipeline by @maxulysse in #1293
• Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in #1297
• Add missing files from Tximport processing by @pinin4fjords in #1302
• Remove redundant gene TPM outputs by @pinin4fjords in #1304
• Strip problematic ifEmpty() by @pinin4fjords in #1317
• Reinstate oncomplete error messages by @pinin4fjords in #1319
• Reinstate pseudoalignment subworkflow config by @pinin4fjords in #1310
• Document FASTP sampling by @pinin4fjords in #1309
• Fix issues with unzipping of GTF/ GFF files without absolute paths by @pinin4fjords in #1312
• Clarify infer strandedness step in subway map and text by @maxulysse in #1307
• Remove push and release triggers from CI by @adamrtalbot in #1321
• Use Github Action to detect file changes instead of custom Python code by @adamrtalbot in #1322
• Update actions/checkout to v4 by @adamrtalbot in #1323
• Overhaul strandedness detection / comparison by @pinin4fjords in #1306
• Move Conda dependencies for local modules to individual environment file by @drpatelh in #1326
• Minor fixes to strandedness settings and messaging by @pinin4fjords in #1325
• Fix tags entries and rename pipeline level tests by @drpatelh in #1324
• Remove tags from all nf-test files by @drpatelh in #1329
• Add nf-test for STAR-RSEM and HISAT2 aligners by @adamrtalbot in #1328
• Update all nf-core/modules and subworkflows by @drpatelh in #1330
• add stub for local modules by @maxulysse in #1331
• Adding stubs everywhere by @maxulysse in #1334
• Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling. by @MatthiasZepper in #1308
• Update Azure Batch guidance by @adamrtalbot in #1340
• Add reference recommendations to usage docs by @lazappi in #1314
• Add rename in the MultiQC report for samples without techreps by @pinin4fjords in #1341
• Use nf-core/setup-nf-test action for portability by @adamrtalbot in #1336
• Factor out preprocessing by @pinin4fjords in #1342
• Fix preprocessing call by @pinin4fjords in #1345
• Reduce resource usage for sort process in bedtools/genomecov by @pinin4fjords in #1350
• Correct conditional for salmon indexing in preprocessing workflow by @pinin4fjords in #1353
• Fix curves in subway map by @maxulysse in #1355
• Assorted fixes to MultiQC usage by @pinin4fjords in #1352
• Work around anchor issue in multiqc by @pinin4fjords in #1357
• Adding stubs at all level by @maxulysse in #1335
• Update test_full.config to restore a static URI for megatests by @pinin4fjords in #1358
• Revert multiqc workaround by @pinin4fjords in #1359
• Move multiqc module prefix for ...

nf-core/rnaseq v3.14.0 - Hassium Honey Badger

What's Changed

• Bump versions for work on 3.14.0 milestone by @pinin4fjords in #1129
• Update action tower launch to v2 by @adamrtalbot in #1135
• Update FastQC and UMItools modules by @mahesh-panchal in #1138
• MultiQC dupRadar custom plot: specify plot_type explicitly by @vladsavelyev in #1137
• Important! Template update for nf-core/tools v2.11 by @nf-core-bot in #1141
• Revert "Update FastQC and UMItools modules" by @pinin4fjords in #1148
• Patch modules to fix #1103 by @drpatelh in #1149
• Interface to kmer size for pseudoaligners by @pinin4fjords in #1144
• Move fasta check back to Groovy by @pinin4fjords in #1143
• Be more flexible on attribute values in GTFs by @pinin4fjords in #1150
• fix to #1150: reinstate conditional by @pinin4fjords in #1151
• Bump container versions for tools using Docker V1 manifest by @drpatelh in #1152
• Prerelease 3.14.0 fixes by @pinin4fjords in #1154
• Add slash to outdir for cloud tests to fix Azure validation… by @drpatelh in #1157
• Bump MultiQC version from 1.17 -> 1.19 by @drpatelh in #1159
• Final prerelease fixes to fix Cloud CI by @drpatelh in #1160
• Dev -> master for 3.14.0 release by @drpatelh in #1156

New Contributors

• @vladsavelyev made their first contribution in #1137

Full Changelog: 3.13.2...3.14.0