Releases: nf-core/rnaseq
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:
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 usingpublic.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:
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:
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
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.
- Users can now select between
- [#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
andparams.extra_star_align_args
prevents parameter clashes in the STAR module - [#940] - Bugfix in
salmon_summarizedexperiment.r
to ensurerbind
doesn't fail whenrowdata
has notx
column. - [#944] - Read clipping using clip_r1, clip_r2, three_prime_clip_r1, three_prime_clip_r2 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.