Rnaseq Versions Save

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

3.14.0

4 months ago

What's Changed

New Contributors

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.2...3.14.0

3.13.2

5 months ago

What's Changed

New Contributors

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.1...3.13.2

3.13.1

5 months ago

What's Changed

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.13.0...3.13.1

3.13.0

5 months ago

What's Changed

New Contributors

Full Changelog: https://github.com/nf-core/rnaseq/compare/3.12.0...3.13.0

3.12.0

11 months ago

[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 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.

3.11.2

1 year ago

[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

3.11.1

1 year ago

[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

3.11.0

1 year ago

[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.
  • [#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.

3.10.1

1 year ago

[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

3.10

1 year ago

[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.