Rnaseq: Question: What is the parameters.settings.json file for?

[sstadick]

[drpatelh]

Hi @sstadick . Here's a link to the original issue that was created to add this file to the nf-core pipeline template. TLDR: It's not being used yet but the idea is to have a central file containing all of the pipeline parameters that can be autofilled in various files in the pipeline, and to add GUI functionality etc.
https://github.com/nf-core/tools/issues/267

[drpatelh]

We have a proof of concept implementation in the pipeline below:
https://github.com/nf-core/hlatyping

Possibly need to finalise this and roll it out to other pipelines!

[sstadick]

First, thanks for he super speedy reply!

That was exactly what I was hoping it was for! It looks like the nf-core launch command can parse it currently and builds up a nextflow run command, but only interactively?

And looking at the main.nf file in hlatypeing, that includes all the helper functions to parse that file, but only to use as the usage message, not actually setting the params variables from it? (looking in the dev branch hla hlatypeing)

[sstadick]

I believe I have answered my questions reading through the issues and PR's you mentioned.

To recap for future visitors and be corrected if I'm wrong:
parameters.settings.json originated from https://nf-co.re/tools#launch-a-pipeline to aid a wizard in generating a params.json file that the pipeline could then be launched with (via the -params-file flag).

It is now also being used to generate the usage messages in the hlatyping pipeline (dev), and may eventually be used for generating the summary's as well.

I was hung up thinking that it could be used in the -params-file option, but it can't.

Overall, super cool and very useful! I will be using it to drive a gui and have a params.json file passed back to me to run. Thanks for your help!

[ewels]

Almost - you can use the one for the rnaseq pipeline already, with the wizard in the nf-core tools package:

$ nf-core launch rnaseq


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'


INFO: Launching nf-core/rnaseq

Main nextflow options

Config profile to use
 -profile [standard]:

Unique name for this nextflow run
 -name [None]:

Work directory for intermediate files
 -w [./work]:

Resume a previous workflow run
 -resume [y/N]:

Release / revision to use
 -r [None]:


Parameter group: Other pipeline parameters
Do you want to change the group's defaults? [y/N]: y

aligner
 --aligner ['star']: hisat2

skip_qc
 --skip_qc [y/N]:

# many more options...

Nextflow command:
  nextflow run nf-core/rnaseq -params-file "/Users/philewels/testing/nfx-params.json"


Do you want to run this command now? [y/N]:

So, the wizard creates a nfx-params.json file that you can use with the nextflow -params-file option.

The pipelines.settings.json file contains all of the pipeline-specific metadata to make this work and will hopefully be used in quite a few other contexts in the future. We're not advertising it a lot yet, as not all pipelines have them and the launch function hasn't been as extensively tested as other features.

I hope this clarifies things!

Phil

[sstadick]

It does! Thank you for the help!