<!subteam^S08MYEKMNTX> I just noticed that in our

.nextflow.config

we havr

--run_busco true

by default, but I don't like that behaviour as it's not intuitive for users to go

--run_busco false

to skip it... and is inconsistent with the others what would be our be our preferred behaviour here? 1. Change just busco back to

--skip_busco

2. Set all BinQC tools to

--skip_<tool>

3. Set all to

false

and have another error check that if you

--skip_binqc false

and all the

run_<troo>

parameters are

false

then we tell user to turn one of them on

I usually prefer when a pipeline is running with default setting. I disliked my (novice) experience with sarek, because variant calling was disabled by default ()in a variant calling pipeline...). Personally, for my using the pipeline, I wouldnt care, but for someone who just wants to run that pipeline that will be in my opinion an unpleasant first experience, its a guaranteed first fail of the pipeline when all binners are turned off by default. Edit: I do agree though that setting a skip_* parameter to true is a bad idea. Optimally that should change.

My personal preference is to have

—run_X

parameters only, and just have them set to true or false depending on what is a sensible default. I don’t really understand the guideline that all boolean flags have to have the same state by default.

I don’t really understand the guideline that all boolean flags have to have the same state by default.

For me because

--run_blah

and

--run_blah true

are two ways of setting the same to true, but

--run_blah false

set it's to false. But given the standard pattern is to run

--run_blah

to turn it true, users do not know how to turn it off. No-where is it described you can specify to a boolean parameter

true

or

false

. Setting

false

is 'internal' knowledge, so to say

1. be most convenient, I think. But inconsistent. Possibly it would be best to change to something like

--binqc_tool

but allow multiple comma separated values? By default e.g.

--binqc_tool busco

and make

--binqc_tool busco,checkm2

and such possible?

We talked about that when adding multiple but I didn't like it due it being error prone

Run by default all three is better than run none, imho.

Eaxctly

I agree that the 3 options should be consistent. But I also don't like that everything is run by default. In some way, CheckM is already outdated and could be could be considered superseeded by CheckM2, so most of the time doesn't really make sense (to me at least) to run it.

On that point, from our discussions with the folk in Denmark doing the Danish Microflora project, they still run CheckM alongside CheckM2 as they find that CheckM2 still does not handle some lineages very well

The other drawback from "run all by default" is run times. With the next version of mag, we will be running 6 binners by default, and that's a lot. So if a user just uses the basic setup (input + outdir) will end up with very long and compute intensive runtimes (2 assemblers * 6 binners * 3 qc tools, prokka on a huge amount of bins, etc)

Agree with Diego... > But given the standard pattern is to run

--run_blah

to turn it true, users do not know how to turn it off. No-where is it described you can specify to a boolean parameter

true

or

false

. Setting

false

is 'internal' knowledge, so to say We can document this in the params descriptions/in the pipeline docs, something like: "all tools are controlled by a parameter called

--run_X

. To disable a tool, change the value of

run_X

to false in your params file or run Nextflow with `--run_X false`" I'm not opposed to enforcing a little reading. Ideally Nextflow would support boolean flags like

argparse

, but I understand why it doesn't.

Hrmmm, OK. I still don't particularly use it (as people still won't read), but I guess I'm being outvoted here and #C078586GZ5X @Daniel Straub are you OK wiht this then, still have something run even if parameter usage is inconsistent?

> are you OK wiht this then, still have something run even if parameter usage is inconsistent? Yes