Pipeline not downloading the Gene_gtf

JihedC / Snakemake_ATAC_2020

Repository for Jianhui's snakemake pipeline

MIT License

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Pipeline not downloading the Gene_gtf #9

Closed JihedC closed 3 years ago

JihedC commented 3 years ago

ComputeMatrix rules does not work because the gtf for genes is not downloaded in the temp/ folder. We need to make sure the rules that downloads it work and is activated.

WJH58 commented 3 years ago

@JihedC I added "GFT" as input so snakemake will force it to be downloaded.

JihedC commented 3 years ago

can you try the pipeline from scratch and see if it works now?

WJH58 commented 3 years ago

@JihedC I have tried the whole pipeline and it works now. gft file has been downloaded in the temp/ folder.

JihedC commented 3 years ago

Ok I will try it on my side, if it works I will close this issue.

JihedC commented 3 years ago

Pipeline ran without problem to get the gtf file