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
Full Changelog: 3.14.0...3.15.0