methylseq - Screaming sloth

MethylSeq pipeline of TOBI lab

v2.6.2 - 2025-07-15

In-house modifications applied to nf-core/methylseq pipeline version v2.6.0

• Added parameter to deactivate PicardMarkduplicates module
• Added parameter to specify which sequencer has been used for PicardMarkduplicates module.
• Reordered the main Bismark Workflow.
• Added the optional Sequencing Saturation plots.
• Picard Markduplicates module has been added to Bismark subworflow(look at the module for more information).
• Bismark filter_non_conversion function has been added to the Bismark subworkflow. It can be activated specifing the flga --filter_non_conversion together with the minimum_count and percentage_cutoff parameters (see nextflow.conf and filternonconversion module for more information). When activated, it creates an output folder where it saves 3 files. The fitlered bam file is then used for the subsequent modules. It needs to be updated with a new version of Bismark (and the corresponding biocontainer) when it is released (there is a bug in the current version, see the issue #688) since now it's not using an official Bismark biocontainer.

- Nextflow
Published by edogiuili 7 months ago