Releases
1.4
phue
released this
20 Nov 12:42
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.
Software updates
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
Pipeline updates
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
Bug fixes
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 )
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