a few minor edits and comments; added the rulegraph image#3
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a few minor edits and comments; added the rulegraph image#3
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gwct
commented
Oct 23, 2025
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| The work directory can be full very quickly, because each time you run a process, it creates a new subdirectory in the `work` directory. If you run the same process multiple times, it will create multiple subdirectories. We recommend setting the work directory to a scratch directory rather than your home or lab share so that it does not fill up your allocation. You should think of everything in the `work` directory as temporary files that can be deleted at any time. | ||
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| ### The `publishDir` directory |
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I think this is ok, but this section could also wait until the develop session
gwct
commented
Oct 23, 2025
| When you run Nextflow, you create a head job that manages the workflow and submits jobs to the local machine or a job scheduler. Each process is run in its own isolated environment, which can be a docker or singularity container, a conda environment, or just the local environment. This means that each process can have its own dependencies and versions of software without interfering with other processes. | ||
| When you run Nextflow, you create a head job that manages the workflow and submits jobs to the local machine or a job scheduler (like SLURM). Each process is run in its own isolated environment, which can be a docker or singularity container, a conda environment, or just the local environment. This means that each process can have its own dependencies and versions of software without interfering with other processes. | ||
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| <!-- Need image diagram of head job submitting child jobs--> |
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Also, is there a way for nextflow to generate an image of the rulegraph? could be good for the example workflows. If not, how does one get a sense for what a workflow does?
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