Open Fadwa7 opened 5 months ago
However, I want it to execute all rules in the Snakefile on the first 4 files, then move to the next 4 files, and so on.
Hello, yeah I been through this before, basically you want snakemake to execute depth first, here are some links to read more: https://github.com/snakemake/snakemake/issues/2595 https://stackoverflow.com/questions/67332350/snakemake-priorities-that-one-sample-finishes-before-next-starts https://stackoverflow.com/questions/64173399/snakemake-tranverse-dag-depth-first https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#priorities
Thank you so much. Can you please explain why parallel-fastq-dump takes the number of cores (--cores) when I run snakemake -s snakefile --cores instead of taking the number of threads I put in the rule? For example, if I put 16 threads in the fetch_sra rule, when I execute snakemake -s snakefile --cores 2, does parallel-fastq-dump split the SRA into 2 chunks?
Thank you in advance
yeah, the number of threads you set on the rule is just a "maximum", since you set --cores 4
on the command line snakemake changes the threads the rules can use to 4, read more here:
https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#threads
Thank you so much
Hi, I am working on a pipeline that downloads SRR files, and to optimize the download time, I opted for your tool. However, I am encountering an issue. I have a list of 143 files, and when I run this command:
And I launch Snakemake with snakemake -s snakefile --cores 4, it processes all files in batches of 4 until it finishes executing the first rule, then it moves to the second rule. However, I want it to execute all rules in the Snakefile on the first 4 files, then move to the next 4 files, and so on.
Do you have any solutions? Thank you in advance.