Belated Dodo

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