A nextflow pipeline for modification calling in nanopore reads.
The current version of Dogme is customized to run on SLURM clusters. You must first install Dorado, Minimap2, samtools, modkit, kallisto, and bustools and add their paths to the dogme.profile file in the project directory. You must also donwload the latest dorado models in specific folder to be defined in the config file.
Prerequisites include installing nextflow, using java/17 or better, installing dogme in an accessible folder, installing modkit, downloading dorado models into a defined folder. By default, nextflow will use the launchdirectory as the place to create its workfolder. You must also create your own long-read kallisto index and t2g file for your genome of interest. You will need to add the path to the genome fasta, the transcriptome gtf, the kallisto index and the kallisto t2g file to your custom config file.
The config file must be updated to the list where the top directory containing the pod5 folder and the pipeline outputs are located as well as the work directory. Ideally the config file would also be in the top directory folder.
Running Dogme on typical dataset can take more than 24 hours, therefore it is recommended to run Dogme within a job or a saved virtual terminal such as screen or Tmux. Change your folder to be where you want Dogme to run (the 'launch' directory), and launch Dogme directly from github using the following command :
nextflow run mortazavilab/dogme -c yourconfig.conf
By default, the pipeline will create several folders within the launch directory such as bams, bedMethyl, fastqs, and kallisto - all of which can be changed in the config file. If you need to resume your work add '-resume' to the nextflow command after deleting the html report and trace files.