- Changed all parameter names to
--local_alignmentoption to run Bismark with the
--localflag 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
--meth_cutoffparameter to change default for
- eg. use
--meth_cutoff 5on the command line or
params.meth_cutoff = 5to require 5 overlapping reads to call a methylation site.
- eg. use
--methyl_kitoption to run MethylDackel with the
--methylKitflag, producing output suitable for the methylKit R package.
- new dependency: hisat2
- new dependency: r-markdown
- Keep memory in GB for samtools, to avoid problems with unit conversion (#99)
- 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)