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nf-core/methylseq: nf-core/methylseq version 1.5 [ Belated Dodo ]

Phil Ewels; Patrick Hüther; Rickard Hammarén; Alexander Peltzer; mashehu; Johannes Alneberg; Sven F.; Paolo Di Tommaso; Colin Davenport; Maxime Garcia; Noirot Céline; Robert Syme; Harshil Patel; Alessia

New features

  • Added multicore support for TrimGalore!
  • Improved the multicore support for Bismark methXtract for more parallelisation (#121)
  • Added --cytosine_report option to tell Bismark to give reports for all cytosines in the genome.
  • Added options --bismark_align_cpu_per_multicore and --bismark_align_cpu_per_multicore to customise how Bismark align --multicore is decided (#124)
Software updates
  • New: pigz 2.3.4
  • Python base 2.7 > 3.7.3
  • FastQC 0.11.8 > 0.11.9
  • TrimGalore! 0.6.4 > 0.6.5
  • HiSAT2 2.1.0 > 2.2.0
  • Bismark 0.22.2 > 0.22.3
  • Qualimap 2.2.2c > 2.2.2d
  • Picard 2.21.3 > 2.22.2
  • MethylDackel 0.4.0 > 0.5.0
  • MultiQC 1.7 > 1.8
Pipeline Updates
  • Fixed bug where the iGenomes config was loaded after the references were set (#121)
  • Removed awsbatch config profile because it is now served by nf-core/configs
  • Tidied up the summary log messages when starting the pipeline
    • Fewer messages saying what you're not doing, sanitised the order of some logs and removed a few things
  • Slightly refactored the code for trimming parameters
  • Updated template to tools 1.9
Bug fixes
  • Fixed error where MethylDackel would consume the Nextflow channels and not work with more than one sample #140

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