WIP: Nextflow

docs/apps/nextflow.md

@@ -6,16 +6,17 @@ tags:
 # Nextflow
 
 Nextflow is a scientific workflow management system for creating scalable,
-portable, and reproducible workflows. 
+portable, and reproducible workflows. It is a groovy-based language for expressing the entire workflow in a single script and also supports running scripts (via script/run/shell directive of Snakemake rule) from other languages such as R, bash and Python. 
+
 
 [TOC]
 
 ## Available 
 
 Versions available on CSC's servers
 
-* Puhti: 21.10.6, 22.04.5, 22.10.1, 23.04.3
-* Mahti: 22.05.0-edge
+* Puhti: 21.10.6, 22.04.5, 22.10.1, 23.04.3, 24.01.0-edge.5903, 24.10.0
+* Mahti: 22.05.0-edge, 24.04.4
 * LUMI: 22.10.4
 
 !!! info "Pay attention to usage of Nextflow version"
@@ -38,13 +39,13 @@ Nextflow is released under the
     module use /appl/local/csc/modulefiles
     ```
 
-Nextflow is activated by loading `nextflow` module as below:
+Nextflow is activated by loading `nextflow` module:
 
 ```bash
 module load nextflow
 ```
 
-Example of loading `nextflow` module with a specific version:
+The default version is usually the latest. Choose the version of the Nextflow depending on the requirements of your own pipeline. It is recommended to load Nextflow module with a version, for the reproducibility point of view.  To load `nextflow` module with a specific version:
 
 ```bash
 module load nextflow/22.04.5
@@ -57,7 +58,7 @@ nextflow -h
 ```
 
 More detailed instructions can be found in
-[CSC's Nextflow tutorial](../support/tutorials/nextflow-puhti.md).
+[CSC's Nextflow tutorial](../support/tutorials/nextflow-tutorial.md).
 
 ## References
 
@@ -69,7 +70,5 @@ computational workflows. Nat. Biotechnol. 35, 316–319 (2017).
 
 ## More information
 
-* [Nextflow documentation](https://www.nextflow.io/docs/latest/index.html)
-* [Running Nextflow on Puhti](../support/tutorials/nextflow-puhti.md)
-* [High-throughput Nextflow workflow using HyperQueue](../support/tutorials/nextflow-hq.md)
-* [Contact CSC Service Desk for technical support](../support/contact.md)
+* [Nextflow official documentation](https://www.nextflow.io/docs/latest/index.html)
+* [CSC Nextflow tutorial](../support/tutorials/nextflow-tutorial.md)

docs/computing/running/throughput.md

@@ -57,7 +57,7 @@ graph TD
     C -->|No| E(Single- or multi-node subtasks?)
     E -->|Single| F(Dependencies between subtasks?)
     E -->|Multi-node| G(<a href='/computing/running/fireworks/'>FireWorks</a>)
-    F -->|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>)
+    F -->|Yes| J(<a href='https://snakemake.readthedocs.io/en/stable/'>Snakemake</a><br><a href='/support/tutorials/nextflow-tutorial/'>Nextflow</a><br><a href='/computing/running/fireworks/'>FireWorks</a>)
     F -->|No| K(<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>)
 ```
 

docs/support/tutorials/index.md

@@ -27,9 +27,7 @@
 * [HyperQueue meta-scheduler](../../apps/hyperqueue.md)
 * [FireWorks workflow manager](../../computing/running/fireworks.md)
 * [How to run many short jobs with GNU Parallel](many.md)
-* [Nextflow tutorial for Puhti (basic)](https://yetulaxman.github.io/Biocontainer/tutorials/nextflow_tutorial.html)
-* [Running Nextflow pipelines on Puhti (advanced)](nextflow-puhti.md)
-* [Running Nextflow workflows using HyperQueue](nextflow-hq.md)
+* [Running Nextflow pipelines](nextflow-tutorial.md)
 * [Running Snakemake pipelines on Puhti](snakemake-puhti.md)
 
 ## Allas

docs/support/tutorials/nextflow-hq.md

@@ -82,8 +82,7 @@ main.nf work
 ## More information
 
 * [General guidelines for high-throughput computing in CSC's HPC environment](../../computing/running/throughput.md)
-* [Basic](https://yetulaxman.github.io/Biocontainer/tutorials/nextflow_tutorial.html)
-  and [advanced Nextflow tutorials for Puhti](nextflow-puhti.md)
+* [CSC Nextflow tutorial](nextflow-tutorial.md)
 * [Official Nextflow documentation](https://www.nextflow.io/docs/latest/index.html)
 * [Official HyperQueue documentation](https://it4innovations.github.io/hyperqueue/stable/)
 * [More information in CSC's HyperQueue documentation](../../apps/hyperqueue.md)