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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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Annotation file asks for columns that shouldn't be needed #540

Closed mmartinezj closed 4 months ago

mmartinezj commented 4 months ago

Hi,

I'm trying to just run FRASER 2.0 with the DROP workflow. On the config file I have set all the run options to false except for the aberrantSplicing, but when i run snakemake --cores 1 -n, it prompts: Incorrect columns in sample annotation file. Missing: ['DNA_VCF_FILE', 'DNA_ID', 'COUNT_MODE', 'COUNT_OVERLAPS', 'STRAND'], which are columns needed for mae, rnaVariantCalling or aberrantExpression. I have created all the files using drop init on the new folder I have created for the project, so I suppose the command isn't calling any other config file from other folder. Thanks in advance!

Best,

Miriam

vyepez88 commented 4 months ago

Hi Miriam, the STRAND column is needed for aberrantSplicing module. We do not have a way of checking the sample annotation's columns only when certain modules are turned on. For the other columns, please create empty columns with those names.

mmartinezj commented 4 months ago

Hi Vicente, adding the columns you mentioned solved this issue, thanks!