nf-core/rnaseq 3.11.0

nf-core/rnaseq v3.11.0 - Radium Rhino

on GitHub

[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

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.

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.