WIP: Add guide for running CWL workflows on Puhti

docs/computing/running/throughput.md

@@ -58,8 +58,8 @@ graph TD
     E -->|Serial| F(<a href='/support/tutorials/many/'>GNU Parallel</a><br><a href='/computing/running/array-jobs/'>Array jobs</a><br><a href='/apps/hyperqueue/'>HyperQueue</a>)
     E -->|Parallel| G(Single- or multinode subtasks?)
     G -->|Single| H(Dependencies between subtasks?)
-    G -->|Multi| I(<a href='/computing/running/fireworks/'>FireWorks</a>)
-    H -->|Yes| J(<a href='https://snakemake.readthedocs.io/en/stable/'>Snakemake</a><br><a href='/support/tutorials/nextflow-puhti/'>Nextflow</a><br><a href='/computing/running/fireworks/'>FireWorks</a>)
+    G -->|Multi| I(<a href='/computing/running/fireworks/'>FireWorks</a><br><a href='/computing/running/toil-cwl-runner/'>Toil-CWL-Runner</a>)
+    H -->|Yes| J(<a href='https://snakemake.readthedocs.io/en/stable/'>Snakemake</a><br><a href='/support/tutorials/nextflow-puhti/'>Nextflow</a><br><a href='/computing/running/fireworks/'>FireWorks</a><br><a href='/computing/running/toil-cwl-runner/'>Toil-CWL-Runner</a>)
     H -->|No| K(<a href='/apps/hyperqueue/'>HyperQueue</a>)
 ```
 
@@ -157,6 +157,8 @@ graph TD
   with `xargs`, see [xargsjob.sh] for example.
 * [FireWorks] is a flexible tool for defining, managing and
   executing workflows with multiple steps and complex dependencies
+* [Toil-CWL-Runner] is an open source workflow manager using the Common
+  Workflow Language open standards
 * [HyperQueue] is a tool for efficient sub-node task scheduling
 * [Nextflow workflows using HyperQueue as an executor] can be leveraged to run
   large workflows involving thousands of processes efficiently
@@ -199,6 +201,7 @@ workflows.
 [HyperQueue]: ../../apps/hyperqueue.md
 [GNU Parallel]: ../../support/tutorials/many.md
 [FireWorks]: fireworks.md
+[Toil-CWL-Runner]: toil-cwl-runner.md
 [contact CSC Service Desk]: ../../support/contact.md
 [Nextflow]: ../../support/tutorials/nextflow-puhti.md
 [Snakemake]: https://snakemake.readthedocs.io/en/stable/

docs/computing/running/toil-cwl-runner.md

@@ -0,0 +1,121 @@
+# Running CWL workflows on Puhti with `toil-cwl-runner`
+
+![CWL Logo](https://raw.githubusercontent.com/common-workflow-language/cwl-website/main/content/assets/img/CWL-Logo-HD-cropped2.png){ width=50% }
+
+The [Common Workflow Language](https://www.commonwl.org/) is a popular set of open standards implemented by several workflow runners and platforms.
+The CWL standards are targeted at creating portable workflows made of command line programs. The steps can be written in any compiled or interpreted language.
+Sub-workflows, optional steps, scatter-gather, and implicit parallelism are just some of the features.
+
+The [Toil workflow system](https://toil.ucsc-cgl.org/) supports running CWL on a variety of schedulers and systems.
+
+This page describes how run CWL worklflows on Puhti using `toil-cwl-runner`, including the usage of `apptainer` to execute any provided Docker-format containers.
+
+## Strengths of the Common Workflow Language standards
+
+- Open standard (free to read, free to contribute to) governed by a [not-for-profit charity which is legally obligated to work in the public interest](https://sfconservancy.org/news/2018/apr/11/cwl-new-member-project/).
+- [Multiple implementations](https://www.commonwl.org/implementations/) of the CWL standards
+- Used in many [different fields of research](https://www.commonwl.org/gallery/)
+- YAML based syntax with [special support in many IDEs](https://www.commonwl.org/tools/#editors)
+- Support, but does not require, software containers. Can also work with conda packages, `module load` environments, and locally available software.
+- CWL's model works hard to keep site-specific deatuls out of the workflow definition. Enabling portability between laptops, clusters, and cloud systems.
+
+## 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 (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.
+
+## Installing `toil-cwl-runner`
+
+Install `toil` with `CWL` plugin.
+```
+module load python-data
+
+cd /projappl/<project_nnnnnnn>
+python -m venv venv
+source venv/bin/activate
+
+pip install -U setuptools wheel
+pip install toil[cwl]
+
+toil-cwl-runner --version
+```
+
+Install `nodejs` which provides helpful tools for debugging `toil` internals.
+```
+cd /projappl/project_nnnnnnn
+wget https://nodejs.org/dist/v18.16.1/node-v18.16.1-linux-x64.tar.xz
+tar -xf node-v18.16.1-linux-x64.tar.xz
+export PATH=$PATH:/projappl/project_nnnnnnn/node-v18.16.1-linux-x64/bin
+```
+
+## Defining CWL workflows
+
+Learning resources
+
+- [Novice CWL tutorial](https://carpentries-incubator.github.io/cwl-novice-tutorial/), includes detailed setup instructions for local editing and running on Microsoft Windows, macOS, and Linux
+- <https://www.commonwl.org/user_guide/>
+
+## Running CWL workflows with `toil-cwl-runner`
+
+!!! Note
+    Singularity containers can't be run in the **login node** or in an **interactive session** due to network constraints.
+
+When you have defined a workflow with `CWL`, you can send it to the cluster using `sbatch`, and then `toil` will start new jobs for each item in the workflow description.
+
+### Preliminary Steps
+Create working directories for `toil`.
+```
+mkdir /projappl/project_nnnnnnn/<job store name>
+mkdir /projappl/project_nnnnnnn/<work dir name>
+mkdir /projappl/project_nnnnnnn/<tmp name>
+```
+
+### Creating the sbatch file
+The `sbatch` file `workflow.sh` will reference the `CWL` file `workflow.cwl` where you have described your workflow steps.
+
+!!! Note
+    See [batch documentation](./creating-job-scripts-puhti.md) on how to fill out the `#SBATCH` values.
+
+`workflow.sh`
+```bash
+#!/bin/sh
+#SBATCH --job-name=<job name here>
+#SBATCH --account=<project_number here>
+#SBATCH --time=01:00:00
+#SBATCH --mem-per-cpu=1G
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=2
+#SBATCH --partition=small
+
+source /projappl/<project_nnnnnnn>/venv/bin/activate
+
+WORKDIR=/projappl/project_nnnnnnn
+SCRATCH=/scratch/project_nnnnnnn
+export TMPDIR=$WORKDIR/tmp
+export TOIL_SLURM_ARGS="--account=project_nnnnnnn --partition=small"
+export CWL_SINGULARITY_CACHE=$WORKDIR/singularity
+unset XDG_RUNTIME_DIR
+
+TOIL_SLURM_ARGS="--account=<project_nnnnnnn> --partition=small" toil-cwl-runner \
+    --jobStore $WORKDIR/<job store name> \
+    --workDir $SCRATCH/<work dir name> \
+    --tmpdir-prefix $TMPDIR/<tmp name> \
+    --batchSystem slurm \
+    $WORKDIR/workflow.cwl \
+    --message "message for job"
+```
+
+Send your workflow to the cluster.
+```
+sbatch workflow.sh
+```
+
+## Monitoring a running workflow
+
+Check the output logs from the main Toil job or
+run `toil status $WORKDIR/<job store name>`.

docs/support/tutorials/index.md

@@ -24,6 +24,7 @@
 * [General high-throughput guidelines](../../computing/running/throughput.md)
 * [Running Nextflow workflows using HyperQueue](nextflow-hq.md)
 * [FireWorks workflow manager](../../computing/running/fireworks.md)
+* [Toil CWL workflow manager](../../computing/running/toil-cwl-runner.md)
 * [How to run many short jobs with GNU Parallel](many.md)
 * [HyperQueue meta-scheduler](../../apps/hyperqueue.md)