Releases: nf-core/rnaseq
Releases · nf-core/rnaseq
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
nf-core/rnaseq v3.13.2 - Cobalt Colt
What's Changed
- Fix pipeline failure when transcript_fasta not provided and skip_gtf_filter is set to TRUE by @RHReynolds in #1126
- Enlarge the sampling range for column determination in FilterGTF script. by @MatthiasZepper in #1127
- Overhaul tximport.r, output length tables by @pinin4fjords in #1123
- Ensure pseudoaligner is set if pseudoalignment is not skipped by @pinin4fjords in #1124
- Dev -> master for 3.13.2 release by @pinin4fjords in #1128
New Contributors
- @RHReynolds made their first contribution in #1126
Full Changelog: 3.13.1...3.13.2
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 #1121
- Dev -> master for 3.13.1 release by @pinin4fjords in #1122
Full Changelog: 3.13.0...3.13.1
nf-core/rnaseq v3.13.0 - Zinc Zebra
What's Changed
- Display a warning when '--extra_star_align_args' are used with RSEM by @MatthiasZepper in #1049
- Update public_aws_ecr.config by @maxulysse in #1048
- Remove public_aws_ecr profile by @adamrtalbot in #1051
- Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #1053
- Update credits for subway map by @maxulysse in #1057
- Use nf-validation plugin for parameter and samplesheet validation by @drpatelh in #1058
- fix copy paste typo by @hmehlan in #1062
- Update untar by @pinin4fjords in #1068
- README.md: Added ref to downstream analyses by @smoe in #1060
- Update the CODE_OF_CONDUCT and CONTRIBUTING with nf-core template 2.10 by @adamrtalbot in #1088
- Reorganise arguments for clearer syntax by @adamrtalbot in #1091
- Reorganise local modules into subfolder/main.nf for consistency by @adamrtalbot in #1083
- Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #1078
- Update usage.md for igenomes warning by @pinin4fjords in #1073
- Update all nf-core/modules in pipeline by @drpatelh in #1093
- update config to enable usage of a custom config by @maxulysse in #1108
- Kallisto quantification by @pinin4fjords in #1106
- Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage by @pinin4fjords in #1107
- Pre-release fixes for 3.13.0 by @pinin4fjords in #1114
- Maxime feedback by @pinin4fjords in #1116
- FIX: Subway map by @maxulysse in #1117
- final updates on subway map by @maxulysse in #1120
- Dev -> Master for 3.13.0 release by @drpatelh in #1113
New Contributors
- @hmehlan made their first contribution in #1062
- @pinin4fjords made their first contribution in #1068
- @smoe made their first contribution in #1060
Full Changelog: 3.12.0...3.13.0