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Monitoring a running toil-cwl-runner
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mr-c committed Jul 11, 2023
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Expand Up @@ -21,10 +21,10 @@ This page describes how run CWL worklflows on Puhti using `toil-cwl-runner`, inc

## Strengths of `toil-cwl-runner`
- Supports sending jobs to Slurm, translating CWL resource requirements to Slurm resources specifications.
- Even when using Slurm, (sub-)tasks do not have to have identical resource requirements.
- Can also run on other batch systems: Grid Engine, Torque, LSF, HTCondor.
- Launches and monitors Slurm jobs for you. Also constructs the apptainer commands.

## Disadvantages for using CWL
- Launches and monitors Slurm jobs for you. Also constructs the `apptainer` commands (or some other software container engine as appropriate: `docker`, `podman`, `singularity`, `udocker`).
- No database needs to be setup.

## Disadvantages for using `toil-cwl-runner`
- Just a workflow runner. Won't manage your data, or keep track of previous workflow runs.
Expand Down Expand Up @@ -114,3 +114,6 @@ sbatch workflow.sh
```

## Monitoring a running workflow

Check the output logs from the main Toil job or
run `toil status $WORKDIR/<job store name>`.

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