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nf-core/rnaseq version 1.4 "Gray Crocus Dachshund"

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@apeltzer apeltzer released this 15 Oct 13:11
· 4640 commits to master since this release
1.4
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Major novel changes include:

  • Support for Salmon as an alternative method to STAR and HISAT2

  • Several improvements in featureCounts handling of types other than exon. It is possible now to handle nuclearRNAseq data. Nuclear RNA has un-spliced RNA, and the whole transcript, including the introns, needs to be counted, e.g. by specifying --fc_count_type transcript.

  • Support for outputting unaligned data to results folders.

  • Added options to skip several steps

    • Skip trimming using --skipTrimming
    • Skip BiotypeQC using --skipBiotypeQC
    • Skip Alignment using --skipAlignment to only use pseudo-alignment using Salmon

Documentation updates

  • Adjust wording of skipped samples in pipeline output
  • Fixed link to guidelines #203
  • Add Citation and Quick Start section to README.md
  • Add in Documentation of the --gff parameter

Reporting Updates

  • Generate MultiQC plots in the results directory #200
  • Get MultiQC to save plots as standalone files
  • Get MultiQC to write out the software versions in a .csv file #185
  • Use file instead of new File to create pipeline_report.{html,txt} files, and properly create subfolders

Pipeline enhancements & fixes

  • Restore SummarizedExperimment object creation in the salmon_merge process avoiding increasing memory with sample size.
  • Fix sample names in feature counts and dupRadar to remove suffixes added in other processes
  • Removed genebody_coverage process #195
  • Implemented Pearsons correlation instead of Euclidean distance #146
  • Add --stringTieIgnoreGTF parameter #206
  • Removed unused stringtie channels for MultiQC
  • Integrate changes in nf-core/tools v1.6 template which resolved #90
  • Moved process convertGFFtoGTF before makeSTARindex #215
  • Change all boolean parameters from snake_case to camelCase and vice versa for value parameters
  • Add SM ReadGroup info for QualiMap compatibility#238
  • Obtain edgeR + dupRadar version information #198 and #112
  • Add --gencode option for compatibility of Salmon and featureCounts biotypes with GENCODE gene annotations
  • Added functionality to accept compressed reference data in the pipeline
  • Check that gtf features are on chromosomes that exist in the genome fasta file #274
  • Maintain all gff features upon gtf conversion (keeps gene_biotype or gene_type to make featureCounts happy)
  • Add SortMeRNA as an optional step to allow rRNA removal #280
  • Minimal adjustment of memory and CPU constraints for clusters with locked memory / CPU relation
  • Cleaned up usage, parameters.settings.json and the nextflow.config

Dependency Updates

  • Dependency list is now sorted appropriately
  • Force matplotlib=3.0.3

Updated Packages

  • Picard 2.20.0 -> 2.21.1
  • bioconductor-dupradar 1.12.1 -> 1.14.0
  • bioconductor-edger 3.24.3 -> 3.26.5
  • gffread 0.9.12 -> 0.11.4
  • trim-galore 0.6.1 -> 0.6.4
  • gffread 0.9.12 -> 0.11.4
  • rseqc 3.0.0 -> 3.0.1
  • R-Base 3.5 -> 3.6.1

Added / Removed Packages

  • Dropped CSVtk in favor of Unix's simple cut and paste utilities
  • Added Salmon 0.14.2
  • Added TXIMeta 1.2.2
  • Added SummarizedExperiment 1.14.0
  • Added SortMeRNA 2.1b
  • Add tximport and summarizedexperiment dependency #171
  • Add Qualimap dependency #202
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