Project directory and documentation comments

[Glenn032787]

Hey Solenne! The pipeline looks great, I just have some suggestions for documentation and project directory structure. The one marked as complete are ones that are in the glennSuggestion branch.

Comments:

• [X] Just a suggestion to have a example_input and src directory for the example fastq/bam files and workflow image respectively.
• [X] Would be good to include a MIT or CC license
• [X] In the ReadMe, I would suggest including either the Github page or the command to install programs that require local installation.
• [X] Change hyperlink for the URL in the readme to make it look more clean
• [ ] #3
• [x] I am not sure what the best practice for nextflow is but it might be good to separate the config files to inputs and parameter config files
• [x] Might be good to include a copy of JuicerTools.jar to the repo? That is what I did in my workflow, it doesn't take up much space but I am not sure if this is best practice.
• [x] #5
• [x] Might be good to suggest minimum memory and time it takes to run since it is a memory/time intensive program (or add a warning saying a step is expected to take a longer time)

[scorreard]

Hi Glenn,

Sorry for the delay, I am working on that on the new release.

• Splitting the config file : We usually don't with nextflow, having one config file is easier and loaded automatically
• JuicerTools.jar : Juicer is no longer a mandatory step in the pipeline, I now use pretext for HiC maps, so it shouldn't crash the pipeline.
• Memory and time for each module (step) are included in the config file, I don't think an additional warning is necessary.

I will try "Running the pipeline with test data" for the new release and if it fails, I will change it to an issue.

Thanks again!

[scorreard]

Closing the issue as the two remaining tasks have been changed to issues