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.

nf-core/rnaseq v3.9 - Niobium Nightingale

[3.9] - 2022-09-30

Enhancements & fixes

• [#746] - Add tin.py output to MultiQC report
• [#841] - Turn --deseq2_vst on by default
• [#853] - Pipeline fails at email step: Failed to invoke workflow.onComplete event handler
• [#857] - Missing parameter required by StringTie if using STAR as aligner
• [#862] - Filter samples that have no reads after trimming
• [#864] - Pre-process transcripts fasta when using --gencode
• Expose additional arguments to UMI-tools as pipeline params: --umitools_bc_pattern2 is required if the UMI is located on read 2. --umitools_umi_separator will often be needed in conjunction with --skip_umi_extract as most other tools such as Illumina's BCL Convert use a colon instead of an underscore to separate the UMIs. The --umitools_grouping_method allows to fine-tune handling of similar but non-identical UMIs.
• Updated pipeline template to nf-core/tools 2.5.1

Parameters

Old parameter	New parameter
	--umitools_bc_pattern2
	--umitools_umi_separator
	--umitools_grouping_method

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
hisat2	2.2.0	2.2.1
multiqc	1.11	1.13
picard	2.26.10	2.27.4

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 version information isn't present.

nf-core/rnaseq v3.8.1 - Plastered Magnesium Mongoose

[3.8.1] - 2022-05-27

• [#834] - nf-core download fails with version 3.8 of the pipeline

nf-core/rnaseq v3.8 - Magnesium Mongoose

[3.8] - 2022-05-25

⚠️ Major enhancements

Fixed a well hidden bug in the UMI processing mode of the pipeline when using --with_umi --aligner star_salmon as reported by Lars Roed Ingerslev. Paired-end BAM files were not appropriately name sorted after umi_tools dedup which ultimately resulted in incorrect reading and quantification with Salmon. If you have used previous versions of the pipeline to analyse paired-end UMI data it will need to be reprocessed using this version of the pipeline. See #828 for more context.

Enhancements & fixes

• [#824] - Add explicit docs for usage of featureCounts in the pipeline
• [#825] - Pipeline fails due to trimming related removal of all reads from a sample
• [#827] - Control generation of --output-stats when running umi-tools dedup
• [#828] - Filter BAM output of UMI-tools dedup before passing to Salmon quant
• Updated pipeline template to nf-core/tools 2.4.1

Parameters

Old parameter	New parameter
	--min_trimmed_reads
	--umitools_dedup_stats