nextflow_dsl2

{nextflow pipeline template}

How to create your nextflow pipeline for APAeval

Read this section, but do NOT include it your final README.

• Copy the whole directory nextflow with its' subfolders to suitable location.
• Rename nextflow to [METHOD]_nextflow, [METHOD] being the name of the tool you're building a workflow for.
• Adjust names and contents of files that appear in this [NOTATION].
• Place any scripts or subworkflows you're going to use into the directories workflow/scripts and workflow/rules, respectively.
• Write your workflow in main.nf.
• Here are the nextflow docs
• General good practices:
  • Test your code with [nextflow main.nf --input <input_file> --other_parameters].
  • Initiate your parameters in nextflow.config.
  • Create a samplesheet.csv file so that all input files and reference files are organized and can be checked whether each file inputted is valid for running downstream process(es).
  • If samples differ in a meaningful way (e.g. single end and paired end samples), it will be great to adjust part of the command for running a software (see example here).
  • If applicable, software has it's own docker container.
  • Add flags for running differnt benchmarking events --run_identification/--run_quantification/--run_differential_analysis
  • Adjust this README.md: Delete this description section and populate the sections below with your awesome experience ;)

[METHOD]

{Description of method, with link to publication and source code.}

Input & pre-processing

{Describe input files and how they will be processed in order for the method to work. Describe how sample tables have to look like, and any other input that is needed (e.g. genome).}

Params

{Describe parameters needed by your METHOD.} {Describe the parameters for running different modes --run_idendification/--run_quantification/--run_differential_analysis}

Output & post-processing

{Describe method output and postprocessing steps if necessary.}

Naming convention for output files: [IDENTIFIER]_[METHOD].[OUTFORMAT]

Notes

{Notes about the METHOD. e.g. Did you have to adjust the method's soure code? }