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

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:

• J Lorent
• Luca Beltrame
• Matthias Zepper
• Maxime Garcia
• Ryan Yordanoff
• Thomas Sandmann

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.
• [#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 and params.extra_star_align_args prevents parameter clashes in the STAR module
• [#940] - Bugfix in salmon_summarizedexperiment.r to ensure rbind doesn't fail when rowdata has no tx 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.

nf-core/rnaseq v3.10.1 - Plastered Rhodium Rudolph

[3.10.1] - 2023-01-05

Enhancements & fixes

• [#919] - Salmon quant not run after FastQ subsampling if index not provided
• [#922] - Passing TrimGalore --hardtrim3 / --hardtrim5 via custom config raises missing output filename error

nf-core/rnaseq v3.10 - Rhodium Rudolph

[3.10] - 2022-12-21

Enhancements & fixes

• Bump minimum Nextflow version from 21.10.3 -> 22.10.1
• Updated pipeline template to nf-core/tools 2.7.2
• [#729] - Add 'auto' option to samplesheet to automatically detect strandedness for samples
• [#889] - Document valid options for --genome parameter
• [#891] - Skip MarkDuplicates when UMIs are used
• [#896] - Remove copyTo call for iGenomes README
• [#897] - Use --skip_preseq by default
• [#898] - Documentation on salmon decoy-aware index creation, gcbias and seqbias
• [#900] - Add --recursive option to fastq_dir_to_samplesheet.py script
• [#902] - check_samplesheet.py script doesn't output optional columns in samplesheet
• [#907] - Add --extra_star_align_args and --extra_salmon_quant_args parameter
• [#912] - Add UMI deduplication before quantification in tube map

Parameters

Old parameter	New parameter
--enable_conda
	--extra_star_align_args
	--extra_salmon_quant_args

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
bbmap	38.93	39.01
bioconductor-dupradar	1.18.0	1.28.0
bioconductor-summarizedexperiment	1.20.0	1.24.0
bioconductor-tximeta	1.8.0	1.12.0
fq		0.9.1
salmon	1.5.2	1.9.0
samtools	1.15.1	1.16.1

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 version information isn't present.