"Nothing to be done" about rasflow HOT 5 CLOSED

Hi Jessie,

Thank you for using RASflow.

Snakemake will always check the final "output" (the input of rule end) and if it finds that the required file is already there, it will do nothing but just say "Nothing to be done."

And the final "output" of QC is: config["FINALOUTPUT"] + "/" + config["PROJECT"]+ "/fastqc/report_quality_control.html" (this can be found in workflow/quality_control.rules), and the first two paras are defined in the config file configs/config_main.yaml. So I suggest to check whether that file is already there (even an empty file with that name) and delete it if it exists. And rerun the workflow.

from rasflow.

Thank you for the detail explanation Xiaokang! This issue is solved, but now I have another question: can we start the pipeline directly from DEA without alignment?

from rasflow.

Yes, but it's tricky. Because you need to make sure that the quantification of transcript/gene is already done and the files are organized in a way that RASflow can recognize (refer to the output from quantify_trans.rules if transcriptome is used as ref, or align_count_genome.rules if genome is used as ref. Then you can use the Snakemake file for DEA:
nice -5 snakemake -s workflow/dea_trans.rules 2>&1 | tee logs/log_dea_trans.txt if you're using transcriptome as reference, or
nice -5 snakemake -s workflow/dea_genome.rules 2>&1 | tee logs/log_dea_genome.txt if the genome is used as reference.

from rasflow.

Problem solved! Thanks a lot Xiaokang!

from rasflow.

Glad to hear that. I'll then close this issue. Feel free to open a new issue when you have another problem.

from rasflow.