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@apeltzer apeltzer released this Sep 21, 2019 · 1 commit to master since this release

v1.0.0 - 2019-09-21

  • Add figures to output documentation
  • Add samtools stats for genome alignments
  • Add seqkit and remove razers
  • Add mirtop and razers tools
  • Adapt code and docs to nf-core template
  • Update tools and Dockerfile/Singularity to match current template

Other

  • Add "protocol" with pre-defined settings
  • Add miRTrace in the pipeline.
  • Switch from SciLifeLab/NGI-smRNAseq to nf-core/smrnaseq.
  • Use Bowtie 1 instead of Bowtie 2 for the alignment to host reference genome.
  • Add option for sequencing center in BAM file.

Dependency Updates

  • openjdk 8.0.144 -> 11.0.1
  • fastqc 0.11.7 -> 0.11.8
  • trim-galore 0.5.0 -> 0.6.2
  • bioconductor-edger 3.20.7 -> 3.26.0
  • bioconductor-limma 3.34.9 -> 3.40.0
  • conda-forge::r-data.table 1.11.4 -> 1.12.2
  • conda-forge::r-gplots 3.0.1 -> 3.0.1.1
  • conda-forge::r-r.methodss3 1.7.1 -> 1.7.1
  • htseq 0.9.1 -> 0.11.2
  • r-markdown 0.9
  • Added mirtop 0.4.18a
  • Removed razers3 3.5.3
  • Added seqkit 0.10.1-1
  • Added seqcluster 1.2.5
  • conda-forge::r-base=3.5.1 -> 3.6.1
  • conda-forge::r-statmod=1.4.30 -> 1.4.32
  • conda-forge::r-markdown=0.9 -> 1.0
  • trim-galore=0.6.2 -> 0.6.3
  • mirtop=0.4.18a -> 0.4.22
  • bioconductor-edger=3.26.0 -> 3.26.5
  • bioconductor-limma=3.40.0 -> 3.40.2
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