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nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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"Nothing to be done" when running locally #31

Open nklier38 opened 3 years ago

nklier38 commented 3 years ago

Following the readme file, I have put the fastq files, a .fa of the reference trnascriptome, and a .gtf corresponding to the transcriptome in the data folder, and edited the config file appropriately.

When first running the pipeline, it installed all of the dependencies without a problem. Now, it gives the following message:

Building DAG of jobs... Nothing to be done.

I cannot identify anything else I have to provide to make it work, am I setting up the config.yaml incorrectly?

saifashraf commented 2 years ago

Hello, I have started using this pipeline lately so a bit late reply. "Nothing to be done" usually comes when output folder named in config file by you is already present in same location. Better you remove same name folder from that location or change the output folder name in config file. Point is one should not name the output folder in config file as one already present in location. Hopefully this will help anyone finding this error. Thanks