nf-core/methylseq: nf-core/methylseq version 1.4 [ Mercury Rattlesnake ]

New features

• Changed all parameter names to snake_case
• Added --local_alignment option to run Bismark with the --local flag to allow soft-clipping of reads.
• Added support for bismark's SLAM-seq mode
• Added support for running bismark with HISAT2 as an aligner option #85
• Added support for centralized configuration profiles nf-core/configs
• Add --meth_cutoff parameter to change default for bismark_methylation_extractor
  • eg. use --meth_cutoff 5 on the command line or params.meth_cutoff = 5 to require 5 overlapping reads to call a methylation site.
• Added --methyl_kit option to run MethylDackel with the --methylKit flag, producing output suitable for the methylKit R package.

• new dependency: hisat2 2.1.0
• new dependency: r-markdown 1.1
• TrimGalore! 0.5.0 > 0.6.4
• Bismark 0.20.0 > 0.22.2
• Bowtie2 2.3.4.3 > 2.3.5
• Picard 2.18.21 > 2.21.3
• Qualimap 2.2.2b > 2.2.2c
• MethylDackel 0.3.0 > 0.4.0

• Keep memory in GB for samtools, to avoid problems with unit conversion (#99)
• Changed params.container for process.container
• Synchronised with version 1.7 of the nf-core/tools template

• Fixed a bug that caused conda dependencies to be resolved very slowly
• Allowed some spare memory in the samtools sort steps, avoiding crashes for some users (#81)