start:software:topical:lifesciences:proteo_transcriptomics

Proteotranscriptomics

Please Note

This workflow is tested and fully functional but could still have some teething problems. Please report any issues at the project site. Be sure to add the version information, which you can obtain by running
$ mflow --version

Prior to starting the workflow you have to fill in the main configuration file. To receive a template configuration which includes description of all parameters use the following command:

$ mflow --show-configuration ProtTrans

This will not only print the sample configuration on screen, but save it to a file ProtTrans.yaml in your working directory, too.

After the configuration is edited, running the workflow is simply done with:

$ mflow --workflow ProtTrans -A <my SLURM account> --configfile <my_config.yaml>

Note, that the run time may exceed the life time of your terminal. To avoid aborting the workflow, you can

  1. start it in nohup mode (see the ''mflow''-documentation)
  2. rely on snakemake to resume unfinished workflow steps the other day

Already submitted jobs will not be aborted, when the terminal running the workflow looses its connection to Mogon.

Should you plan on running a genome guided and a genome free run make sure to only start the second approach after finishing the rule for trim galore on the first approach.
  • start/software/topical/lifesciences/proteo_transcriptomics.txt
  • Last modified: 2021/04/22 12:40
  • by chotting