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-test to module by @pinin4fjords in #1362
• Animate subway map by @maxulysse in #1361
• Snapshot all files (content or file name when not stable) by @maxulysse in #1360
• Fixing failing tests and updating modules once more by @maxulysse in #1363
• Clarify design formula and blind dispersion estimation by @pmoris in #1367
• Clarify docs on different tximport count files by @pmoris in #1366
• Bump versions for 3.15.0 by @pinin4fjords in #1370
• Apply Maxime's changelog edits by @pinin4fjords in #1371
• Bump tximeta/tximport for gene table row names fix by @pinin4fjords in #1372
• [skip ci] Dev -> Master for 3.15.0 by @drpatelh in #1258

New Contributors

• @lazappi made their first contribution in #1314
• @pmoris made their first contribution in #1367

Full Changelog: 3.14.0...3.15.0