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talkowski-lab / gnomad-sv-pipeline

Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
https://broad.io/gnomad_sv
MIT License
36 stars 14 forks source link

Usage questions #1

Open celalp opened 5 years ago

celalp commented 5 years ago

Hi,

Thanks for making all the code public. This is not really an issue but more of a usage question. I would like to be able to repeat some/all of the steps in another (but much smaller) disease cohort that I'm working on. However I do not have firecloud or WDL execution platform.

Is it possible to include a step by step script/command list for the analysis? Or at least the order of the WDL files to run in each module. Even a basic order (in terms of programs and scripts) would be very helpful.

Thanks Alper

yoyosef commented 5 years ago

Hi @celalp

I'm in the same situation,

I'm finding reading their supplementary material useful, which includes a summary of each module, but I haven't delved deep into the code yet.

image

Thanks Yosef

cccnrc commented 4 years ago

Hi,

Thanks for making all the code public. This is not really an issue but more of a usage question. I would like to be able to repeat some/all of the steps in another (but much smaller) disease cohort that I'm working on. However I do not have firecloud or WDL execution platform.

Is it possible to include a step by step script/command list for the analysis? Or at least the order of the WDL files to run in each module. Even a basic order (in terms of programs and scripts) would be very helpful.

Thanks Alper

Yes, I agree, is it possible to have a master or similar to know the order and the input required?