RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
Define where the pipeline should find input data and save output data.
Reference genome related files and options required for the workflow.
Options to adjust read trimming criteria.
Options for filtering reads prior to alignment
Options for processing reads with unique molecular identifiers
Options to adjust parameters and filtering criteria for read alignments.
Additional output files produces as intermediates that can be saved
Additional quality control options.
Options to skip various steps within the workflow.
Parameters used to describe centralised config profiles. These should not be edited.
Set the top limit for requested resources for any single job.
Less common options for the pipeline, typically set in a config file.