Releases | Open Source Science

rnaseq - nf-core/rnaseq v3.20.0 - Iridium Impala

What's Changed

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

New Contributors

@GallVp made their first contribution in https://github.com/nf-core/rnaseq/pull/1573
@idot made their first contribution in https://github.com/nf-core/rnaseq/pull/1571

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.19.0...3.20.0

- Nextflow
Published by maxulysse 6 months ago

rnaseq - nf-core/rnaseq v3.19.0 - Tungsten Turtle

What's Changed

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

New Contributors

@davidecarlson made their first contribution in https://github.com/nf-core/rnaseq/pull/1508
@AlenaNik made their first contribution in https://github.com/nf-core/rnaseq/pull/1518
@delagoya made their first contribution in https://github.com/nf-core/rnaseq/pull/1521
@glichtenstein made their first contribution in https://github.com/nf-core/rnaseq/pull/1528
@fntlnz made their first contribution in https://github.com/nf-core/rnaseq/pull/1553
@atrigila made their first contribution in https://github.com/nf-core/rnaseq/pull/1550

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.18.0...3.19.0

- Nextflow
Published by pinin4fjords 9 months ago

rnaseq - nf-core/rnaseq v3.18.0 - Lithium Lynx

What's Changed

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

New Contributors

@LorenzoS96 made their first contribution in https://github.com/nf-core/rnaseq/pull/1447
@siddharthab made their first contribution in https://github.com/nf-core/rnaseq/pull/1369

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.17.0...3.18.0

- Nextflow
Published by pinin4fjords about 1 year ago

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

New Contributors

@pabloaledo made their first contribution in https://github.com/nf-core/rnaseq/pull/1414

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.16.1...3.17.0

- Nextflow
Published by pinin4fjords over 1 year ago

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

What's Changed

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

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.16.0...3.16.1

- Nextflow
Published by pinin4fjords over 1 year ago

rnaseq - nf-core/rnaseq v3.16.0 - Fire Ferret

What's Changed

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

New Contributors

@egreenberg7 made their first contribution in https://github.com/nf-core/rnaseq/pull/1388

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.15.1...3.16.0

- Nextflow
Published by maxulysse over 1 year ago

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

What's Changed

Bump pipeline version to 3.16.0dev by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1374
Fix issues with R modules changing sample names by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1380
Massive conda modules update by @maxulysse in https://github.com/nf-core/rnaseq/pull/1381
Slight fixes for rnaseq preprocessing by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1382
Prerelease 3.15.1 version bumps by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1383
Master merge by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1385
Dev -> Master for 3.15.1 by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1384

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.15.0...3.15.1

- Nextflow
Published by pinin4fjords over 1 year ago

rnaseq - nf-core/rnaseq v3.15.0 - Aluminium Axolotl

What's Changed

Bump pipeline version to 3.15.0dev by @drpatelh in https://github.com/nf-core/rnaseq/pull/1180
update qualimap/rnaseq by @maxulysse in https://github.com/nf-core/rnaseq/pull/1186
Delete lib directory and replace with utils_* subworkflows by @drpatelh in https://github.com/nf-core/rnaseq/pull/1197
Replace modules.config with more modular config files per module/subworkflow/workflow by @drpatelh in https://github.com/nf-core/rnaseq/pull/1199
Important! Template update for nf-core/tools v2.12 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1201
Remove lib directory and modules.config by @drpatelh in https://github.com/nf-core/rnaseq/pull/1206
CHORES: Update all modules by @maxulysse in https://github.com/nf-core/rnaseq/pull/1212
Use pseudoalignment subworkflow components from nf-core/modules by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1210
Pass transcriptome fasta through to samtools stats by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1213
Bump umitools + delocalise prepareforrsem by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1214
Delocalise catadditionalfasta by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1216
chore: Emiller88 => edmundmiller by @edmundmiller in https://github.com/nf-core/rnaseq/pull/1217
Important! Template update for nf-core/tools v2.13 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1218
nf-test at the pipeline level by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1220
Reuse bbsplit index and don't keep overwriting by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1226
Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1229
Add all nf-core modules and CI/CD and all nf-tests to everything by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1221
Update sortmerna usage by @maxulysse in https://github.com/nf-core/rnaseq/pull/1231
Adding tests for stargenomegenerateigenomes by @maxulysse in https://github.com/nf-core/rnaseq/pull/1232
Switch to genomecov from nf-core by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1234
Add nf-test to local module GTF_FILTER by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1236
nf-test: utilsnfcorernaseq_pipeline tests by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1235
add nf-tests for staralignigenomes by @maxulysse in https://github.com/nf-core/rnaseq/pull/1233
nf-test for PREPROCESSTRANSCRIPTSFASTA_GENCODE by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1238
Fix concurrency error in Github CI workflow by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1237
ALIGN_STAR - add nf-test tests by @maxulysse in https://github.com/nf-core/rnaseq/pull/1239
Swtich to dupradar from nf-core by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1242
Add nf-tests for deseq2_qc local module by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1241
Fix genomes params usage by @maxulysse in https://github.com/nf-core/rnaseq/pull/1240
Add gtf2bed tests by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1244
nf test quantify rsem by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1245
nf-test for module MULTIQCCUSTOMBIOTYPE by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1243
nf-test prepare_genome by @maxulysse in https://github.com/nf-core/rnaseq/pull/1247
Replace deseq2qc paths by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1251
Make README usage consistent with docs/usage.md by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1228
Remove all tags.yml files by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1250
Include nf-tests for rsemmergecounts module by @robsyme in https://github.com/nf-core/rnaseq/pull/1249
nf-test quantify pseudoalignment by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1246
Update CHANGELOG by @drpatelh in https://github.com/nf-core/rnaseq/pull/1260
Try to fix CI pipeline AGAIN by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1262
Small updates noticed during code review by @drpatelh in https://github.com/nf-core/rnaseq/pull/1265
Delete unecessary tags from nf.test files for modules and subworkflows by @drpatelh in https://github.com/nf-core/rnaseq/pull/1266
Add more tests for PREPARE_GENOME by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1261
Fixup: Add GHA files back into include statement of Github workflow change detection by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1264
Update trimming subworkflow to include more tests by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1271
Delocalise pseudo quant workflow by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1278
Update bammarkduplicatespicard subworkflow by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1274
Simple pipeline level nf-tests by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1272
Add new testing strategy based on nf-test files by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1253
Add psueudoaligner pipeline level tests to test suite by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1279
Reorganise pipeline tests into flat structure by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1280
Fix CHANGELOG error by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1282
Increase contents of default.main.nf.test.snap by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1283
Improved ext.args consolidation for STAR and TRIMGALORE by @MatthiasZepper in https://github.com/nf-core/rnaseq/pull/1248
Fix genomeAttribute usage by @maxulysse in https://github.com/nf-core/rnaseq/pull/1252
fix(subworkflow): update utilsnfcorepipeline by @maxulysse in https://github.com/nf-core/rnaseq/pull/1293
Important! Template update for nf-core/tools v2.14.1 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1297
Add missing files from Tximport processing by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1302
Remove redundant gene TPM outputs by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1304
Strip problematic ifEmpty() by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1317
Reinstate oncomplete error messages by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1319
Reinstate pseudoalignment subworkflow config by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1310
Document FASTP sampling by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1309
Fix issues with unzipping of GTF/ GFF files without absolute paths by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1312
Clarify infer strandedness step in subway map and text by @maxulysse in https://github.com/nf-core/rnaseq/pull/1307
Remove push and release triggers from CI by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1321
Use Github Action to detect file changes instead of custom Python code by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1322
Update actions/checkout to v4 by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1323
Overhaul strandedness detection / comparison by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1306
Move Conda dependencies for local modules to individual environment file by @drpatelh in https://github.com/nf-core/rnaseq/pull/1326
Minor fixes to strandedness settings and messaging by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1325
Fix tags entries and rename pipeline level tests by @drpatelh in https://github.com/nf-core/rnaseq/pull/1324
Remove tags from all nf-test files by @drpatelh in https://github.com/nf-core/rnaseq/pull/1329
Add nf-test for STAR-RSEM and HISAT2 aligners by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1328
Update all nf-core/modules and subworkflows by @drpatelh in https://github.com/nf-core/rnaseq/pull/1330
add stub for local modules by @maxulysse in https://github.com/nf-core/rnaseq/pull/1331
Adding stubs everywhere by @maxulysse in https://github.com/nf-core/rnaseq/pull/1334
Various MultiQC issues: FastQC sections for raw and trimmed reads // umi-tools dedup and extraction plots, custom content styling. by @MatthiasZepper in https://github.com/nf-core/rnaseq/pull/1308
Update Azure Batch guidance by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1340
Add reference recommendations to usage docs by @lazappi in https://github.com/nf-core/rnaseq/pull/1314
Add rename in the MultiQC report for samples without techreps by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1341
Use nf-core/setup-nf-test action for portability by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1336
Factor out preprocessing by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1342
Fix preprocessing call by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1345
Reduce resource usage for sort process in bedtools/genomecov by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1350
Correct conditional for salmon indexing in preprocessing workflow by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1353
Fix curves in subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1355
Assorted fixes to MultiQC usage by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1352
Work around anchor issue in multiqc by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1357
Adding stubs at all level by @maxulysse in https://github.com/nf-core/rnaseq/pull/1335
Update test_full.config to restore a static URI for megatests by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1358
Revert multiqc workaround by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1359
Move multiqc module prefix for nf-test to module by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1362
Animate subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1361
Snapshot all files (content or file name when not stable) by @maxulysse in https://github.com/nf-core/rnaseq/pull/1360
Fixing failing tests and updating modules once more by @maxulysse in https://github.com/nf-core/rnaseq/pull/1363
Clarify design formula and blind dispersion estimation by @pmoris in https://github.com/nf-core/rnaseq/pull/1367
Clarify docs on different tximport count files by @pmoris in https://github.com/nf-core/rnaseq/pull/1366
Bump versions for 3.15.0 by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1370
Apply Maxime's changelog edits by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1371
Bump tximeta/tximport for gene table row names fix by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1372
[skip ci] Dev -> Master for 3.15.0 by @drpatelh in https://github.com/nf-core/rnaseq/pull/1258

New Contributors

@lazappi made their first contribution in https://github.com/nf-core/rnaseq/pull/1314
@pmoris made their first contribution in https://github.com/nf-core/rnaseq/pull/1367

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.14.0...3.15.0

- Nextflow
Published by pinin4fjords over 1 year ago

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

What's Changed

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

New Contributors

@vladsavelyev made their first contribution in https://github.com/nf-core/rnaseq/pull/1137

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.2...3.14.0

- Nextflow
Published by drpatelh about 2 years ago

rnaseq - nf-core/rnaseq v3.13.2 - Cobalt Colt

What's Changed

Fix pipeline failure when transcriptfasta not provided and skipgtf_filter is set to TRUE by @RHReynolds in https://github.com/nf-core/rnaseq/pull/1126
Enlarge the sampling range for column determination in FilterGTF script. by @MatthiasZepper in https://github.com/nf-core/rnaseq/pull/1127
Overhaul tximport.r, output length tables by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1123
Ensure pseudoaligner is set if pseudoalignment is not skipped by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1124
Dev -> master for 3.13.2 release by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1128

New Contributors

@RHReynolds made their first contribution in https://github.com/nf-core/rnaseq/pull/1126

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.1...3.13.2

- Nextflow
Published by pinin4fjords over 2 years ago

rnaseq - nf-core/rnaseq v3.13.1 - Ferrous Foal

What's Changed

Changes for 3.13.1 patch release incl. igenomes star fix by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1121
Dev -> master for 3.13.1 release by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1122

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.0...3.13.1

- Nextflow
Published by pinin4fjords over 2 years ago

rnaseq - nf-core/rnaseq v3.13.0 - Zinc Zebra

What's Changed

Display a warning when '--extrastaralign_args' are used with RSEM by @MatthiasZepper in https://github.com/nf-core/rnaseq/pull/1049
Update publicawsecr.config by @maxulysse in https://github.com/nf-core/rnaseq/pull/1048
Remove publicawsecr profile by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1051
Important! Template update for nf-core/tools v2.9 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1053
Update credits for subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1057
Use nf-validation plugin for parameter and samplesheet validation by @drpatelh in https://github.com/nf-core/rnaseq/pull/1058
fix copy paste typo by @hmehlan in https://github.com/nf-core/rnaseq/pull/1062
Update untar by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1068
README.md: Added ref to downstream analyses by @smoe in https://github.com/nf-core/rnaseq/pull/1060
Update the CODEOFCONDUCT and CONTRIBUTING with nf-core template 2.10 by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1088
Reorganise arguments for clearer syntax by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1091
Reorganise local modules into subfolder/main.nf for consistency by @adamrtalbot in https://github.com/nf-core/rnaseq/pull/1083
Important! Template update for nf-core/tools v2.10 by @nf-core-bot in https://github.com/nf-core/rnaseq/pull/1078
Update usage.md for igenomes warning by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1073
Update all nf-core/modules in pipeline by @drpatelh in https://github.com/nf-core/rnaseq/pull/1093
update config to enable usage of a custom config by @maxulysse in https://github.com/nf-core/rnaseq/pull/1108
Kallisto quantification by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1106
Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1107
Pre-release fixes for 3.13.0 by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1114
Maxime feedback by @pinin4fjords in https://github.com/nf-core/rnaseq/pull/1116
FIX: Subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1117
final updates on subway map by @maxulysse in https://github.com/nf-core/rnaseq/pull/1120
Dev -> Master for 3.13.0 release by @drpatelh in https://github.com/nf-core/rnaseq/pull/1113

New Contributors

@hmehlan made their first contribution in https://github.com/nf-core/rnaseq/pull/1062
@pinin4fjords made their first contribution in https://github.com/nf-core/rnaseq/pull/1068
@smoe made their first contribution in https://github.com/nf-core/rnaseq/pull/1060

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.12.0...3.13.0

- Nextflow
Published by pinin4fjords over 2 years ago

rnaseq - nf-core/rnaseq v3.12.0 - Osmium Octopus

[3.12.0] - 2023-06-02

Credits

Special thanks to the following for their contributions to the release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

[#1011] - FastQ files from UMI-tools not being passed to fastp
[#1018] - Ability to skip both alignment and pseudo-alignment to only run pre-processing QC steps.
PR #1016 - Updated pipeline template to nf-core/tools 2.8
PR #1025 - Add public_aws_ecr.config to source mulled containers when using public.ecr.aws Docker Biocontainer registry
PR #1038 - Updated error log for count values when supplying --additional_fasta
PR #1042 - revert samtools_sort modules to no memory assignement

Parameters

| Old parameter | New parameter | | ------------- | ------------------------- | | | --skip_pseudo_alignment |

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | fastp | 0.23.2 | 0.23.4 | | samtools | 1.16.1 | 1.17 |

NB: Dependency has been updated if both old and new version information is present.

NB: Dependency has been added if just the new version information is present.

NB: Dependency has been removed if new version information isn't present.

- Nextflow
Published by drpatelh over 2 years ago

rnaseq - nf-core/rnaseq v3.11.2 - Resurrected Radium Rhino

[3.11.2] - 2023-04-25

Credits

Special thanks to the following for their contributions to the release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

[#1003] - FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX is launched multiple times and fails

- Nextflow
Published by drpatelh almost 3 years ago

rnaseq - nf-core/rnaseq v3.11.1 - Plastered Radium Rhino

[3.11.1] - 2023-03-31

Credits

Special thanks to the following for their code contributions to the release:

Enhancements & fixes

[#987] - Fix issue with incorrect cacheing of test datasets during CI/CD
[#988] - DESEQ2_QC_STAR_SALMON fails when sample names have many components
Remove wait: false option from Tower Actions which is the default
Fix release trigger for full-sized multi-cloud tests
Adding [ci fast] to commit message now skips all tests except for standard -profile test pipeline run

- Nextflow
Published by drpatelh almost 3 years ago

rnaseq - nf-core/rnaseq v3.11.0 - Radium Rhino

[3.11.0] - 2023-03-30

Credits

Special thanks to the following for their code contributions to the release:

Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.

Enhancements & fixes

Add infrastructure and CI for multi-cloud full-sized tests run via Nextflow Tower (see #981)
Added fastp support.
- Users can now select between --trimmer trimgalore (default) and --trimmer fastp.
- Trim Galore! specific pipeline parameters have been deprecated: --clip_r1, --clip_r2, --three_prime_clip_r1, --three_prime_clip_r2 and --trim_nextseq
- Any additional options can now be specified via the --extra_trimgalore_args and --extra_fastp_args parameters, respectively.
[#663] - Alternative trimming step for polyA/T removal
[#781] - Add Warning for poly(A) libraries
[#878] - Allow tabs in fasta header when creating decoys for salmon index
[#931] - Save transcriptome BAM files when using --save_umi_intermeds / --save_align_intermeds
[#934] - Union of ext.args and params.extra_star_align_args prevents parameter clashes in the STAR module
[#940] - Bugfix in salmon_summarizedexperiment.r to ensure rbind doesn't fail when rowdata has no tx column.
[#944] - Read clipping using clipr1, clipr2, threeprimeclipr1, threeprimeclipr2 disabled in 3.10
[#956] - Implement 'auto' as default strandedness argument in fastq_dir_to_samplesheet.py script
[#960] - Failure with awsbatch when running processes that are using executor: local
[#961] - Add warnings to STDOUT for all skipped and failed strandedness check samples
[#975] - SALMON_INDEX runs when using --aligner star_rsem even if samples have explicit strandedness
Remove HISAT2 from automated AWS full-sized tests

Parameters

| Old parameter | New parameter | | ----------------------- | ------------------------- | | | --trimmer | | | --extra_trimgalore_args | | --clip_r1 | | | --clip_r2 | | | --three_prime_clip_r1 | | | --three_prime_clip_r2 | | | --tracedir | | | --trim_nextseq | |

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | | ----------- | ----------- | ----------- | | fastp | | 0.23.2 | | multiqc | 1.13 | 1.14 | | picard | 2.27.4 | 3.0.0 | | salmon | 1.9.0 | 1.10.1 | | umi_tools | 1.1.2 | 1.1.4 |

NB: Dependency has been updated if both old and new version information is present.

NB: Dependency has been added if just the new version information is present.

NB: Dependency has been removed if new version information isn't present.

- Nextflow
Published by drpatelh almost 3 years ago

rnaseq - nf-core/rnaseq v3.10.1 - Plastered Rhodium Rudolph

[3.10.1] - 2023-01-05

Enhancements & fixes

[#919] - Salmon quant not run after FastQ subsampling if index not provided
[#922] - Passing TrimGalore --hardtrim3 / --hardtrim5 via custom config raises missing output filename error

- Nextflow
Published by drpatelh about 3 years ago

rnaseq - nf-core/rnaseq v3.10 - Rhodium Rudolph

[3.10] - 2022-12-21

Enhancements & fixes

Bump minimum Nextflow version from 21.10.3 -> 22.10.1
Updated pipeline template to nf-core/tools 2.7.2
[#729] - Add 'auto' option to samplesheet to automatically detect strandedness for samples
[#889] - Document valid options for --genome parameter
[#891] - Skip MarkDuplicates when UMIs are used
[#896] - Remove copyTo call for iGenomes README
[#897] - Use --skip_preseq by default
[#898] - Documentation on salmon decoy-aware index creation, gcbias and seqbias
[#900] - Add --recursive option to fastq_dir_to_samplesheet.py script
[#902] - check_samplesheet.py script doesn't output optional columns in samplesheet
[#907] - Add --extra_star_align_args and --extra_salmon_quant_args parameter
[#912] - Add UMI deduplication before quantification in tube map

Parameters

| Old parameter | New parameter | | ---------------- | --------------------------- | | --enable_conda | | | | --extra_star_align_args | | | --extra_salmon_quant_args |

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | | ----------------------------------- | ----------- | ----------- | | bbmap | 38.93 | 39.01 | | bioconductor-dupradar | 1.18.0 | 1.28.0 | | bioconductor-summarizedexperiment | 1.20.0 | 1.24.0 | | bioconductor-tximeta | 1.8.0 | 1.12.0 | | fq | | 0.9.1 | | salmon | 1.5.2 | 1.9.0 | | samtools | 1.15.1 | 1.16.1 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh about 3 years ago

rnaseq - nf-core/rnaseq v3.9 - Niobium Nightingale

[3.9] - 2022-09-30

Enhancements & fixes

[#746] - Add tin.py output to MultiQC report
[#841] - Turn --deseq2_vst on by default
[#853] - Pipeline fails at email step: Failed to invoke workflow.onComplete event handler
[#857] - Missing parameter required by StringTie if using STAR as aligner
[#862] - Filter samples that have no reads after trimming
[#864] - Pre-process transcripts fasta when using --gencode
Expose additional arguments to UMI-tools as pipeline params: --umitools_bc_pattern2 is required if the UMI is located on read 2. --umitools_umi_separator will often be needed in conjunction with --skip_umi_extract as most other tools such as Illumina's BCL Convert use a colon instead of an underscore to separate the UMIs. The --umitools_grouping_method allows to fine-tune handling of similar but non-identical UMIs.
Updated pipeline template to nf-core/tools 2.5.1

Parameters

| Old parameter | New parameter | | ------------- | ---------------------------- | | | --umitools_bc_pattern2 | | | --umitools_umi_separator | | | --umitools_grouping_method |

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | | ---------- | ----------- | ----------- | | hisat2 | 2.2.0 | 2.2.1 | | multiqc | 1.11 | 1.13 | | picard | 2.26.10 | 2.27.4 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh over 3 years ago

rnaseq - nf-core/rnaseq v3.8.1 - Plastered Magnesium Mongoose

[3.8.1] - 2022-05-27

[#834] - nf-core download fails with version 3.8 of the pipeline

- Nextflow
Published by drpatelh over 3 years ago

rnaseq - nf-core/rnaseq v3.8 - Magnesium Mongoose

[3.8] - 2022-05-25

:warning: Major enhancements

Fixed a well hidden bug in the UMI processing mode of the pipeline when using --with_umi --aligner star_salmon as reported by Lars Roed Ingerslev. Paired-end BAM files were not appropriately name sorted after umi_tools dedup which ultimately resulted in incorrect reading and quantification with Salmon. If you have used previous versions of the pipeline to analyse paired-end UMI data it will need to be reprocessed using this version of the pipeline. See #828 for more context.

Enhancements & fixes

[#824] - Add explicit docs for usage of featureCounts in the pipeline
[#825] - Pipeline fails due to trimming related removal of all reads from a sample
[#827] - Control generation of --output-stats when running umi-tools dedup
[#828] - Filter BAM output of UMI-tools dedup before passing to Salmon quant
Updated pipeline template to nf-core/tools 2.4.1

Parameters

| Old parameter | New parameter | | ------------- | ------------------------ | | | --min_trimmed_reads | | | --umitools_dedup_stats |

- Nextflow
Published by drpatelh over 3 years ago

rnaseq - nf-core/rnaseq v3.7 - Iron Iguana

[3.7] - 2022-05-03

:warning: Major enhancements

Updated default STAR version to latest available (2.7.10a; see #808)
Vanilla Linux Docker container changed from biocontainers/biocontainers:v1.2.0_cv1 to ubuntu:20.04 to fix issues observed on GCP (see #764)

Enhancements & fixes

[#762] - Explicitly set --skip_bbsplit false with --bbsplit_fasta_list to use BBSplit
[#764] - Test fails when using GCP due to missing tools in the basic biocontainer
[#765] - Add docs for the usage of nf-core/rnaseq with prokaryotic data
[#775] - Incorrect columns in Salmon transcript files
[#791] - Add outputs for umitools dedup summary stats
[#797] - Add --skip_umi_extract to account for pre-existing UMIs header embeddings.
[#798] - Decompress transcript fasta error
[#799] - Issue with using --retain_unpaired with the FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE module
[#802] - --bam_csi_index error generated if --skip_alignment specified
[#808] - Auto-detect usage of Illumina iGenomes reference
[#809] - Add metro map for pipeline
[#814] - Use decimal values for --min_mapped_reads
Updated pipeline template to nf-core/tools 2.3.2

Parameters

| Old parameter | New parameter | | ------------- | -------------------- | | | --skip_umi_extract |

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | | ----------- | ----------- | ----------- | | samtools | 1.14 | 1.15.1 | | star | 2.6.1d | 2.7.10a | | stringtie | 2.1.7 | 2.2.1 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh almost 4 years ago

rnaseq - nf-core/rnaseq v3.6 - Platinum Platypus

[3.6] - 2022-03-04

Enhancements & fixes

nf-core/tools#1415 - Make --outdir a mandatory parameter
[#734] - Is a vulnerable picard still used ? log4j vulnerability
[#744] - Auto-detect and raise error if CSI is required for BAM indexing
[#750] - Optionally ignore R1 / R2 after UMI extraction process
[#752] - How to set publishing mode for all processes?
[#753] - Add warning when user provides --transcript_fasta
[#754] - DESeq2 QC issue linked to --count_col parameter
[#755] - Rename RSEMPREPAREREFERENCETRANSCRIPTS process
[#759] - Empty lines in samplesheet.csv cause a crash
[#769] - Do not run RSeQC tin.py by default

Parameters

| Old parameter | New parameter | |-------------------------------|---------------------------------------| | | --publish_dir_mode | | | --umi_discard_read |

NB: Parameter has been updated if both old and new parameter information is present.

NB: Parameter has been added if just the new parameter information is present.

NB: Parameter has been removed if new parameter information isn't present.

- Nextflow
Published by drpatelh almost 4 years ago

rnaseq - nf-core/rnaseq v3.5 - Copper Chameleon

[3.5] - 2021-12-17

Enhancements & fixes

Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
- Removed --publish_dir_mode as it is no longer required for the new syntax
Bump minimum Nextflow version from 21.04.0 -> 21.10.3
Updated pipeline template to nf-core/tools 2.2
[#664] - Conflict of library names for technical replicates
[#720] - KeyError 'geneid' in salmontx2gene.py
[#724] - Deal with warnings generated when native NF processes are used
[#725] - Untar needs --no-same-owner on DNAnexus
[#727] - Fix transcriptome staging issues on DNAnexus for rsem/prepareference
[#728] - Add RSeQC TIN.py as a quality metric for the pipeline

- Nextflow
Published by drpatelh about 4 years ago

rnaseq - nf-core/rnaseq v3.4 - Aluminium Aardvark

[3.4] - 2021-10-05

Enhancements & fixes

Software version(s) will now be reported for every module imported during a given pipeline execution
Added python3 shebang to appropriate scripts in bin/ directory
[#407] - Filter mouse reads from PDX samples
[#570] - Update SortMeRNA to use SilvaDB 138 (for commercial use)
[#690] - Error with post-trimmed read 2 sample names from FastQC in MultiQC
[#693] - Cutadapt version missing from MultiQC report
[#697] - pipelinereport.{txt,html} missing from pipelineinfo directory
[#705] - Sample sheet error check false positive

Parameters

| Old parameter | New parameter | |-----------------------------|--------------------------------| | | --bbsplit_fasta_list | | | --bbsplit_index | | | --save_bbsplit_reads | | | --skip_bbsplit |

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | |---------------|-------------|-------------| | bbmap | | 38.93 | | hisat2 | 2.2.0 | 2.2.1 | | picard | 2.23.9 | 2.25.7 | | salmon | 1.4.0 | 1.5.2 | | samtools | 1.12 | 1.13 | | sortmerna | 4.2.0 | 4.3.4 | | trim-galore | 0.6.6 | 0.6.7 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh over 4 years ago

rnaseq - nf-core/rnaseq v3.3 - Bronze Bear

[3.3] - 2021-07-29

Enhancements & fixes

Updated pipeline template to nf-core/tools 2.1
[#556] - Genome index isn't recreated with --additionalfasta unless --starindex false
[#668] - Salmon quant with UMI-tools does not work
[#674] - Launch pipeline regex fails

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | |-------------|-------------|-------------| | samtools | 1.10 | 1.12 | | stringtie | 2.1.4 | 2.1.7 | | umi_tools | 1.1.1 | 1.1.2 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh over 4 years ago

rnaseq - nf-core/rnaseq v3.2 - Copper Flamingo

[3.2] - 2021-06-18

Enhancements & fixes

Removed workflow to download data from public databases in favour of using nf-core/fetchngs
Added a stand-alone Python script bin/fastq_dir_to_samplesheet.py to auto-create samplesheet from a directory of FastQ files
Added docs about overwriting default container definitions to use latest versions e.g. Pangolin
[#637] - Add --salmon_quant_libtype parameter to provide the --libType option to salmon quantification
[#645] - Remove trailing slash from params.igenomes_base
[#649] - DESeq2 fails with only one sample
[#652] - Results files have incorrect file names
[nf-core/viralrecon#201] - Conditional include are not expected to work

Parameters

| Old parameter | New parameter | |-----------------------------|--------------------------------| | --public_data_ids | | | --skip_sra_fastq_download | | | | --salmon_quant_libtype |

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present.

- Nextflow
Published by drpatelh over 4 years ago

rnaseq - nf-core/rnaseq v3.1 - Lead Alligator

[3.1] - 2021-05-13

:warning: Major enhancements

Samplesheet format has changed from group,replicate,fastq_1,fastq_2,strandedness to sample,fastq_1,fastq_2,strandedness
- This gives users the flexibility to name their samples however they wish (see #550)
- PCA generated by DESeq2 will now be monochrome and will not be grouped by using the replicate id
Updated Nextflow version to v21.04.0 (see nextflow#572)
Restructure pipeline scripts into modules/, subworkflows/ and workflows/ directories

Enhancements & fixes

Updated pipeline template to nf-core/tools 1.14
Initial implementation of a standardised samplesheet JSON schema to use with user interfaces and for validation
Only FastQ files that require to be concatenated will be passed to CAT_FASTQ process
[#449] - --genomeSAindexNbases will now be auto-calculated before building STAR indices
[#460] - Auto-detect and bypass featureCounts execution if biotype doesn't exist in GTF
[#544] - Update test-dataset for pipeline
[#553] - Make tximport output files using all the samples; identified by @j-andrews7
[#561] - Add gene symbols to merged output; identified by @grst
[#563] - samplesheet.csv merge error
[#567] - Update docs to mention trimgalore core usage nuances
[#568] - --star_index argument is ignored with --aligner star_rsem option
[#569] - nextflow edge release documentation for running 3.0
[#575] - Remove duplicated salmon output files
[#576] - umi_tools dedup : Run before salmon to dedup counts
[#582] - Generate a separate bigwig tracks for each strand
[#583] - Samtools error during run requires use of BAM CSI index
[#585] - Clarify salmon uncertainty for some transcripts
[#604] - Additional fasta with GENCODE annotation results in biotype error
[#610] - save R objects as RDS
[#619] - implicit declaration of the workflow in main
[#629] - Add and fix EditorConfig linting in entire pipeline
[nf-core/modules#423] - Replace publish_by_id module option to publish_by_meta
[nextflow#2060] - Pipeline execution hang when native task fail to be submitted

Parameters

| Old parameter | New parameter | |-----------------------------|--------------------------------| | --hisat_build_memory | --hisat2_build_memory | | --gtf_count_type | --featurecounts_feature_type | | --gtf_group_features_type | --featurecounts_group_type | | | --bam_csi_index | | | --schema_ignore_params | | | --show_hidden_params | | | --validate_params | | --clusterOptions | |

NB: Parameter has been updated if both old and new parameter information is present. NB: Parameter has been added if just the new parameter information is present. NB: Parameter has been removed if parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | |-------------|-------------|-------------| | bedtools | 2.29.2 | 2.30.0 | | multiqc | 1.9 | 1.10.1 | | preseq | 2.0.3 | 3.1.2 |

NB: Dependency has been updated if both old and new version information is present. NB: Dependency has been added if just the new version information is present. NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh almost 5 years ago

rnaseq - nf-core/rnaseq v3.0 - Silver Shark

[3.0] - 2020-12-15

:warning: Major enhancements

You will need to install Nextflow >=20.11.0-edge to run the pipeline. If you are using Singularity, then features introduced in that release now enable the pipeline to directly download Singularity images hosted by Biocontainers as opposed to performing a conversion from Docker images (see #496).
The previous default of aligning BAM files using STAR and quantifying using featureCounts (--aligner star) has been removed. The new default is to align with STAR and quantify using Salmon (--aligner star_salmon).
- This decision was made primarily because of the limitations of featureCounts to appropriately quantify gene expression data. Please see Zhao et al., 2015 and Soneson et al., 2015).
For similar reasons, quantification will not be performed if using --aligner hisat2 due to the lack of an appropriate option to calculate accurate expression estimates from HISAT2 derived genomic alignments.
- This pipeline option is still available for those who have a preference for the alignment, QC and other types of downstream analysis compatible with the output of HISAT2. No gene-level quantification results will be generated.
- In a future release we hope to add back quantitation for HISAT2 using different tools.

Enhancements & fixes

Updated pipeline template to nf-core/tools 1.12.1
Bumped Nextflow version 20.07.1 -> 20.11.0-edge
Added UCSC bedClip module to restrict bedGraph file coordinates to chromosome boundaries
Check if Bioconda and conda-forge channels are set-up correctly when running with -profile conda
Use rsem-prepare-reference and not gffread to create transcriptome fasta file
[#494] - Issue running rnaseq v2.0 (DSL2) with test profile
[#496] - Direct download of Singularity images via HTTPS
[#498] - Significantly different versions of STAR in star_rsem (2.7.6a) and star (2.6.1d)
[#499] - Use of salmon counts for DESeq2
[#500, #509] - Error with AWS batch params
[#511] - rsem/star index fails with large genome
[#515] - Add decoy-aware indexing for salmon
[#516] - Unexpected error [InvocationTargetException]
[#525] - sraidsto_runinfo.py UnicodeEncodeError

Parameters

| Old parameter | New parameter | |------------------------------|---------------------------------------| | --fc_extra_attributes | --gtf_extra_attributes | | --fc_group_features | --gtf_group_features | | --fc_count_type | --gtf_count_type | | --fc_group_features_type | --gtf_group_features_type | | | --singularity_pull_docker_container | | --skip_featurecounts | |

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if parameter information isn't present.

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | |-------------------------------------|-------------|-------------| | bioconductor-summarizedexperiment | 1.18.1 | 1.20.0 | | bioconductor-tximeta | 1.6.3 | 1.8.0 | | picard | 2.23.8 | 2.23.9 | | requests | | 2.24.0 | | salmon | 1.3.0 | 1.4.0 | | ucsc-bedclip | | 377 | | umi_tools | 1.0.1 | 1.1.1 |

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh about 5 years ago

rnaseq - nf-core/rnaseq v2.0 - Titanium Tiger

[2.0] - 2020-11-12

Major enhancements

Pipeline has been re-implemented in Nextflow DSL2
All software containers are now exclusively obtained from Biocontainers
Added a separate workflow to download FastQ files via SRA, ENA or GEO ids and to auto-create the input samplesheet (ENA FTP; see --public_data_ids parameter)
Added and refined a Groovy lib/ of functions that include the automatic rendering of parameters defined in the JSON schema for the help and summary log information
Replace edgeR with DESeq2 for the generation of PCA and heatmaps (also included in the MultiQC report)
Creation of bigWig coverage files using BEDTools and bedGraphToBigWig
[#70] - Added new genome mapping and quantification route with RSEM via the --aligner star_rsem parameter
[#72] - Samples skipped due to low alignment reported in the MultiQC report
[#73, #435] - UMI barcode support
[#91] - Ability to concatenate multiple runs of the same samples via the input samplesheet
[#123] - The primary input for the pipeline has changed from --reads glob to samplesheet --input. See usage docs.
[#197] - Samples failing strand-specificity checks reported in the MultiQC report
[#227] - Removal of ribosomal RNA via SortMeRNA
[#419] - Add --additional_fasta parameter to provide ERCC spike-ins, transgenes such as GFP or CAR-T as additional sequences to align to

Other enhancements & fixes

Updated pipeline template to nf-core/tools 1.11
Optimise MultiQC configuration for faster run-time on huge sample numbers
Add information about SILVA licensing when removing rRNA to usage.md
Fixed ansi colours for pipeline summary, added summary logs of alignment results
[#281] - Add nag to cite the pipeline in summary
[#302] - Fixed MDS plot axis labels
[#338] - Add option for turning on/off STAR command line option (--sjdbGTFfile)
[#344] - Added multi-core TrimGalore support
[#351] - Fixes missing Qualimap parameter -p
[#353] - Fixes an issue where MultiQC fails to run with --skip_biotype_qc option
[#357] - Fixes broken links
[#362] - Fix error with gzipped annotation file
[#384] - Changed SortMeRNA reference dbs path to use stable URLs (v4.2.0)
[#396] - Deterministic mapping for STAR aligner
[#412] - Fix Qualimap not being passed on correct strand-specificity parameter
[#413] - Fix STAR unmapped reads not output
[#434] - Fix typo reported for work-dir
[#437] - FastQC uses correct number of threads now
[#440] - Fixed issue where featureCounts process fails when setting --fc_count_type to gene
[#452] - Fix --gff input bug
[#345] - Fixes label name in FastQC process
[#391] - Make publishDir mode configurable
[#431] - Update AWS GitHub actions workflow with organization level secrets
[#435] - Fix a bug where gzipped references were not extracted when --additional_fasta was not specified
[#435] - Fix a bug where merging of RSEM output would fail if only one fastq provided as input
[#435] - Correct RSEM output name (was saving counts but calling them TPMs; now saving both properly labelled)
[#436] - Fix a bug where the RSEM reference could not be built
[#458] - Fix TMP_DIR for process MarkDuplicates and Qualimap

Parameters

Updated

| Old parameter | New parameter | |------------------------------|----------------------------| | --reads | --input | | --igenomesIgnore | --igenomes_ignore | | --removeRiboRNA | --remove_ribo_rna | | --rRNA_database_manifest | --ribo_database_manifest | | --save_nonrRNA_reads | --save_non_ribo_reads | | --saveAlignedIntermediates | --save_align_intermeds | | --saveReference | --save_reference | | --saveTrimmed | --save_trimmed | | --saveUnaligned | --save_unaligned | | --skipAlignment | --skip_alignment | | --skipBiotypeQC | --skip_biotype_qc | | --skipDupRadar | --skip_dupradar | | --skipFastQC | --skip_fastqc | | --skipMultiQC | --skip_multiqc | | --skipPreseq | --skip_preseq | | --skipQC | --skip_qc | | --skipQualimap | --skip_qualimap | | --skipRseQC | --skip_rseqc | | --skipTrimming | --skip_trimming | | --stringTieIgnoreGTF | --stringtie_ignore_gtf |

Added

--additional_fasta - FASTA file to concatenate to genome FASTA file e.g. containing spike-in sequences
--deseq2_vst - Use vst transformation instead of rlog with DESeq2
--enable_conda - Run this workflow with Conda. You can also use '-profile conda' instead of providing this parameter
--min_mapped_reads - Minimum percentage of uniquely mapped reads below which samples are removed from further processing
--multiqc_title - MultiQC report title. Printed as page header, used for filename if not otherwise specified
--public_data_ids - File containing SRA/ENA/GEO identifiers one per line in order to download their associated FastQ files
--publish_dir_mode - Method used to save pipeline results to output directory
--rsem_index - Path to directory or tar.gz archive for pre-built RSEM index
--rseqc_modules - Specify the RSeQC modules to run
--save_merged_fastq - Save FastQ files after merging re-sequenced libraries in the results directory
--save_umi_intermeds - If this option is specified, intermediate FastQ and BAM files produced by UMI-tools are also saved in the results directory
--skip_bigwig - Skip bigWig file creation
--skip_deseq2_qc - Skip DESeq2 PCA and heatmap plotting
--skip_featurecounts - Skip featureCounts
--skip_markduplicates - Skip picard MarkDuplicates step
--skip_sra_fastq_download - Only download metadata for public data database ids and don't download the FastQ files
--skip_stringtie - Skip StringTie
--star_ignore_sjdbgtf - See #338
--umitools_bc_pattern - The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the first 6 nucleotides of the read are from the UMI
--umitools_extract_method - UMI pattern to use. Can be either 'string' (default) or 'regex'
--with_umi - Enable UMI-based read deduplication

Removed

--awsqueue can now be provided via nf-core/configs if using AWS
--awsregion can now be provided via nf-core/configs if using AWS
--compressedReference now auto-detected
--markdup_java_options in favour of updating centrally on nf-core/modules
--project parameter from old NGI template
--readPaths is not required since these are provided from the input samplesheet
--sampleLevel not required
--singleEnd is now auto-detected from the input samplesheet
--skipEdgeR qc not performed by DESeq2 instead
--star_memory in favour of updating centrally on nf-core/modules if required
Strandedness is now specified at the sample-level via the input samplesheet
- --forwardStranded
- --reverseStranded
- --unStranded
- --pico

Software dependencies

Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Dependency | Old version | New version | |-------------------------------------|-------------|-------------| | bioconductor-dupradar | 1.14.0 | 1.18.0 | | bioconductor-summarizedexperiment | 1.14.0 | 1.18.1 | | bioconductor-tximeta | 1.2.2 | 1.6.3 | | fastqc | 0.11.8 | 0.11.9 | | gffread | 0.11.4 | 0.12.1 | | hisat2 | 2.1.0 | 2.2.0 | | multiqc | 1.7 | 1.9 | | picard | 2.21.1 | 2.23.8 | | qualimap | 2.2.2c | 2.2.2d | | r-base | 3.6.1 | 4.0.3 | | salmon | 0.14.2 | 1.3.0 | | samtools | 1.9 | 1.10 | | sortmerna | 2.1b | 4.2.0 | | stringtie | 2.0 | 2.1.4 | | subread | 1.6.4 | 2.0.1 | | trim-galore | 0.6.4 | 0.6.6 | | bedtools | - | 2.29.2 | | bioconductor-biocparallel | - | 1.22.0 | | bioconductor-complexheatmap | - | 2.4.2 | | bioconductor-deseq2 | - | 1.28.0 | | bioconductor-tximport | - | 1.16.0 | | perl | - | 5.26.2 | | python | - | 3.8.3 | | r-ggplot2 | - | 3.3.2 | | r-optparse | - | 1.6.6 | | r-pheatmap | - | 1.0.12 | | r-rcolorbrewer | - | 1.12 | | rsem | - | 1.3.3 | | ucsc-bedgraphtobigwig | - | 377 | | `umitools| - | 1.0.1 | |bioconductor-edger| - | - | |deeptools| - | - | |matplotlib| - | - | |r-data.table| - | - | |r-gplots| - | - | |r-markdown` | - | - |

NB: Dependency has been updated if both old and new version information is present.
NB: Dependency has been added if just the new version information is present.
NB: Dependency has been removed if version information isn't present.

- Nextflow
Published by drpatelh over 5 years ago

rnaseq - nf-core/rnaseq version 1.4.2

Version 1.4.2

Minor version release for keeping Git History in sync
No changes with respect to 1.4.1 on pipeline level

- Nextflow
Published by apeltzer over 6 years ago

rnaseq - nf-core/rnaseq version 1.4.1

Version 1.4.1

Major novel changes include:

Update igenomes.config with NCBI GRCh38 and most recent UCSC genomes
Set autoMounts = true by default for singularity profile

Pipeline enhancements & fixes

Fixed parameter warnings #316 and 318
Fixed #307 - Confusing Info Printout about GFF and GTF

- Nextflow
Published by apeltzer over 6 years ago

rnaseq - nf-core/rnaseq version 1.4 "Gray Crocus Dachshund"

Major novel changes include:

Support for Salmon as an alternative method to STAR and HISAT2
Several improvements in featureCounts handling of types other than exon. It is possible now to handle nuclearRNAseq data. Nuclear RNA has un-spliced RNA, and the whole transcript, including the introns, needs to be counted, e.g. by specifying --fc_count_type transcript.
Support for outputting unaligned data to results folders.
Added options to skip several steps
- Skip trimming using --skipTrimming
- Skip BiotypeQC using --skipBiotypeQC
- Skip Alignment using --skipAlignment to only use pseudo-alignment using Salmon

Documentation updates

Adjust wording of skipped samples in pipeline output
Fixed link to guidelines #203
Add Citation and Quick Start section to README.md
Add in Documentation of the --gff parameter

Reporting Updates

Generate MultiQC plots in the results directory #200
Get MultiQC to save plots as standalone files
Get MultiQC to write out the software versions in a .csv file #185
Use file instead of new File to create pipeline_report.{html,txt} files, and properly create subfolders

Pipeline enhancements & fixes

Restore SummarizedExperimment object creation in the salmon_merge process avoiding increasing memory with sample size.
Fix sample names in feature counts and dupRadar to remove suffixes added in other processes
Removed genebody_coverage process #195
Implemented Pearsons correlation instead of Euclidean distance #146
Add --stringTieIgnoreGTF parameter #206
Removed unused stringtie channels for MultiQC
Integrate changes in nf-core/tools v1.6 template which resolved #90
Moved process convertGFFtoGTF before makeSTARindex #215
Change all boolean parameters from snake_case to camelCase and vice versa for value parameters
Add SM ReadGroup info for QualiMap compatibility#238
Obtain edgeR + dupRadar version information #198 and #112
Add --gencode option for compatibility of Salmon and featureCounts biotypes with GENCODE gene annotations
Added functionality to accept compressed reference data in the pipeline
Check that gtf features are on chromosomes that exist in the genome fasta file #274
Maintain all gff features upon gtf conversion (keeps gene_biotype or gene_type to make featureCounts happy)
Add SortMeRNA as an optional step to allow rRNA removal #280
Minimal adjustment of memory and CPU constraints for clusters with locked memory / CPU relation
Cleaned up usage, parameters.settings.json and the nextflow.config

Dependency Updates

Dependency list is now sorted appropriately
Force matplotlib=3.0.3

Updated Packages

Picard 2.20.0 -> 2.21.1
bioconductor-dupradar 1.12.1 -> 1.14.0
bioconductor-edger 3.24.3 -> 3.26.5
gffread 0.9.12 -> 0.11.4
trim-galore 0.6.1 -> 0.6.4
gffread 0.9.12 -> 0.11.4
rseqc 3.0.0 -> 3.0.1
R-Base 3.5 -> 3.6.1

Added / Removed Packages

Dropped CSVtk in favor of Unix's simple cut and paste utilities
Added Salmon 0.14.2
Added TXIMeta 1.2.2
Added SummarizedExperiment 1.14.0
Added SortMeRNA 2.1b
Add tximport and summarizedexperiment dependency #171
Add Qualimap dependency #202

- Nextflow
Published by apeltzer over 6 years ago

rnaseq - nf-core/rnaseq version 1.3

Pipeline Updates

Added configurable options to specify group attributes for featureCounts #144
Added support for RSeqC 3.0 #148
Added a parameters.settings.json file for use with the new nf-core launch helper tool.
Centralized all configuration profiles using nf-core/configs
Fixed all centralized configs for offline usage
Hide %dup in multiqc report

Bug fixes

Fixing HISAT2 Index Building for large reference genomes #153
Fixing HISAT2 BAM sorting using more memory than available on the system
Fixing MarkDuplicates memory consumption issues following #179

Dependency Updates

RSeQC 2.6.4 -> 3.0.0
Picard 2.18.15 -> 2.18.23
r-data.table 1.11.4 -> 1.12.0
r-markdown 0.8 -> 0.9
csvtk 0.15.0 -> 0.17.0
stringtie 1.3.4 -> 1.3.5
subread 1.6.2 -> 1.6.4
gffread 0.9.9 -> 0.9.12
multiqc 1.6 -> 1.7

- Nextflow
Published by apeltzer almost 7 years ago

rnaseq - nf-core/rnaseq version 1.2

Pipeline updates

Removed some outdated documentation about non-existent features
Config refactoring and code cleaning
Added a --fcExtraAttributes option to specify more than ENSEMBL gene names in featureCounts
Remove legacy rseqc strandRule config code. #119
Added STRINGTIE ballgown output to results folder #125
HiSAT index build now requests 200GB memory, enough to use the exons / splice junction option for building.
- Added documentation about the --hisatBuildMemory option.
BAM indices are stored and re-used between processes #71

Bug Fixes

Fixed conda bug which caused problems with environment resolution due to changes in bioconda #113
Fixed wrong gffread command line #117
Added cpus = 1 to workflow summary process #130

- Nextflow
Published by ewels about 7 years ago

rnaseq - nf-core/rnaseq version 1.1

Pipeline updates

Wrote docs and made minor tweaks to the --skip_qc and associated options
Removed the depreciated uppmax-modules config profile
Updated the hebbe config profile to use the new withName syntax too
Use new workflow.manifest variables in the pipeline script
Updated minimum nextflow version to 0.32.0

Software updates

FastQC 0.11.7 > 0.11.8
STAR 2.6.1a > 2.6.1b
Picard 2.18.11 > 2.18.14
Deeptools 3.1.1 > 3.1.4

Bug Fixes

#77: Added back executor = 'local' for the workflow_summary_mqc
#95: Check if task.memory is false instead of null
#97: Resolved edge-case where numeric sample IDs are parsed as numbers causing some samples to be incorrectly overwritten.

- Nextflow
Published by ewels over 7 years ago

rnaseq - nf-core/rnaseq version 1.0

Initial release of nf-core/rnaseq! 🎉

This release marks the point where the pipeline was moved from SciLifeLab/NGI-RNAseq over to the new nf-core community, at nf-core/rnaseq. You can view the previous changelog at SciLifeLab/NGI-RNAseq/CHANGELOG.md

In addition to porting to the new nf-core community, the pipeline has had a number of major changes in this version. There have been 157 commits by 16 different contributors covering 70 different files in the pipeline: 7,357 additions and 8,236 deletions!

In summary, the main changes are:

Rebranding and renaming throughout the pipeline to nf-core
Updating many parts of the pipeline config and style to meet nf-core standards
Support for GFF files in addition to GTF files
- Just use --gff instead of --gtf when specifying a file path
New command line options to skip various quality control steps
More safety checks when launching a pipeline
- Several new sanity checks - for example, that the specified reference genome exists
Improved performance with memory usage (especially STAR and Picard)
New BigWig file outputs for plotting coverage across the genome
Refactored gene body coverage calculation, now much faster and using much less memory
Bugfixes in the MultiQC process to avoid edge cases where it wouldn't run
MultiQC report now automatically attached to the email sent when the pipeline completes
New testing method, with data on GitHub
- Now run pipeline with -profile test instead of using bash scripts
Rewritten continuous integration tests with Travis CI
New explicit support for Singularity containers
Improved MultiQC support for DupRadar and featureCounts
- Now works for all users instead of just NGI Stockholm
New configuration for use on AWS batch
Updated config syntax to support latest versions of Nextflow
Built-in support for a number of new local HPC systems
- CCGA, GIS, UCT HEX, updates to UPPMAX, CFC, BINAC, Hebbe, c3se
Slightly improved documentation (more updates to come)
Updated software packages

...and many more minor tweaks.

Thanks to everyone who has worked on this release!

- Nextflow
Published by ewels over 7 years ago

Recent Releases of rnaseq

rnaseq - nf-core/rnaseq v3.20.0 - Iridium Impala

What's Changed

New Contributors

rnaseq - nf-core/rnaseq v3.19.0 - Tungsten Turtle

What's Changed

New Contributors

rnaseq - nf-core/rnaseq v3.18.0 - Lithium Lynx

What's Changed

New Contributors

rnaseq - nf-core/rnaseq v3.17.0 - Neon Newt

What's Changed

New Contributors

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

What's Changed

rnaseq - nf-core/rnaseq v3.16.0 - Fire Ferret

What's Changed

New Contributors

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

What's Changed

rnaseq - nf-core/rnaseq v3.15.0 - Aluminium Axolotl

What's Changed

New Contributors

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

What's Changed

New Contributors

rnaseq - nf-core/rnaseq v3.13.2 - Cobalt Colt

What's Changed

New Contributors

rnaseq - nf-core/rnaseq v3.13.1 - Ferrous Foal

What's Changed

rnaseq - nf-core/rnaseq v3.13.0 - Zinc Zebra

What's Changed

New Contributors

rnaseq - nf-core/rnaseq v3.12.0 - Osmium Octopus

[3.12.0] - 2023-06-02

Credits

Enhancements & fixes

Parameters

Software dependencies

rnaseq - nf-core/rnaseq v3.11.2 - Resurrected Radium Rhino

[3.11.2] - 2023-04-25

Credits

Enhancements & fixes

rnaseq - nf-core/rnaseq v3.11.1 - Plastered Radium Rhino

[3.11.1] - 2023-03-31

Credits

Enhancements & fixes

rnaseq - nf-core/rnaseq v3.11.0 - Radium Rhino

[3.11.0] - 2023-03-30

Credits

Enhancements & fixes

Parameters

Software dependencies

rnaseq - nf-core/rnaseq v3.10.1 - Plastered Rhodium Rudolph

[3.10.1] - 2023-01-05

Enhancements & fixes

rnaseq - nf-core/rnaseq v3.10 - Rhodium Rudolph

[3.10] - 2022-12-21

Enhancements & fixes

Parameters

Software dependencies

rnaseq - nf-core/rnaseq v3.9 - Niobium Nightingale

[3.9] - 2022-09-30

Enhancements & fixes

Parameters

Software dependencies

rnaseq - nf-core/rnaseq v3.8.1 - Plastered Magnesium Mongoose

[3.8.1] - 2022-05-27

rnaseq - nf-core/rnaseq v3.8 - Magnesium Mongoose

[3.8] - 2022-05-25

:warning: Major enhancements

Enhancements & fixes

Parameters

rnaseq - nf-core/rnaseq v3.7 - Iron Iguana

[3.7] - 2022-05-03

:warning: Major enhancements

Enhancements & fixes

Parameters

Software dependencies

rnaseq - nf-core/rnaseq v3.2 - Copper Flamingo

rnaseq - nf-core/rnaseq v3.1 - Lead Alligator