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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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No Overview.html file after aberrantSplicing analysis with DROP v1.4.0 #554

Closed mmartinezj closed 3 weeks ago

mmartinezj commented 3 weeks ago

Hello,

I have run just the aberrantSplicing module and got the following html files: html_files

As you can see, the index, readme, counting datasets and fraser datasets htmls are present, but neither the overview html nor the folder "Scripts_AberrantSplicing_Overview_files" is present. But after checking the log file, I haven't been able to found any error regarding this. Also I have tried to run "snakemake Scripts_AberrantSplicing_Overview_R", but I got an error: run_overview

If you need any more info or the log file, please let me know. Thanks in advance!

Best,

Miriam

Update: I have run the aberrantSplicing module with the dataset that comes with drop and it doesn't generate the overview html either in case this is of any use.

AtaJadidAhari commented 3 weeks ago

Hi Miriam,

Those files are created by another rule after rule aberrantSplicnig, i.e. from rule Index and that's why when running only aberrantSplicnig rule, they are not produced. You can create them by running: snakemake AberrantSplicing_Overview_R instead of snakemake Scripts_AberrantSplicing_Overview_R

mmartinezj commented 3 weeks ago

Hi Ata,

thanks for the quick response. I am running snakemake Scripts_AberrantSplicing_Overview_R on the project folder. As I can see from the logs and time it is taking, this command is rerunning the whole module again. Is this the behaviour it should have or it should just have taken the info/files already computed and just generated a html?

vyepez88 commented 3 weeks ago

Hi Miriam, please use the --rerun-triggers mtime every time you want to rerun the aberrant splicing pipeline and set recount: false in the config file (unless you want to recount the data)

mmartinezj commented 3 weeks ago

Thank you Ata and Vicente. Both of the solutions worked!