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

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:

• Adam Talbot
• Esha Joshi
• Ghepardo
• Matthias Zepper
• Maxime Garcia
• Rob Syme

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.

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:

• Jonathan Manning
• Maxime Garcia
• Rob Syme
• W. Lee Pang

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

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:

• Adam Talbot
• Rob Syme
• suhrig

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