BinAC/Software/Nextflow: Difference between revisions
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= Description = |
= Description = |
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Nextflow is a scientific workflow system predominantly used for bioinformatic data analyses. |
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This documentation also addresses nf-core, which is a community effort to collect a curated set of analysis pipelines built using Nextflow. |
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= Installation = |
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There is no environment module for Nextflow on the BinAC. We encourage users to install Nextflow via Miniconda. |
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As Nextflow is often used with nf-core pipelines, we also recommend to install the nf-core tools. |
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The following commands will create a new Conda environment that provides Nextflow and nf-core tools. |
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It also sets a Singularity cache directory where all Singularity containers are stored. |
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<pre> |
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conda create --name nf-core python nf-core nextflow |
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echo "export NXF_SINGULARITY_CACHEDIR=/beegfs/work/container/apptainer_cache" >> ~/.bashrc |
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echo "export SINGULARITY_CACHEDIR=/beegfs/work/tu_iioba01/apptainer_cache " >> ~/.bashrc |
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source ~/.bashrc |
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conda activate nf-core |
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</pre> |
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= Usage = |
= Usage = |
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== Install a nf-core pipeline == |
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You could start and run pipelines now and the pipeline will pull all containers themselves. |
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<b>But</b> we experienced problems when a pipeline started more than one job that pulls the same image. |
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Thus we recommend to download the pipeline first using the nf-core tools. |
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In this example we will use the rnaseq pipeline. If you need another pipeline, |
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<pre> |
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nf-core download -x none -d -u amend --container-system singularity -r 3.14.0 rnaseq |
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</pre> |
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nf-core tools can download pipelines and also download Singularity containers. |
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Revision as of 10:28, 12 August 2024
Description
Nextflow is a scientific workflow system predominantly used for bioinformatic data analyses. This documentation also addresses nf-core, which is a community effort to collect a curated set of analysis pipelines built using Nextflow.
Installation
There is no environment module for Nextflow on the BinAC. We encourage users to install Nextflow via Miniconda. As Nextflow is often used with nf-core pipelines, we also recommend to install the nf-core tools.
The following commands will create a new Conda environment that provides Nextflow and nf-core tools. It also sets a Singularity cache directory where all Singularity containers are stored.
conda create --name nf-core python nf-core nextflow echo "export NXF_SINGULARITY_CACHEDIR=/beegfs/work/container/apptainer_cache" >> ~/.bashrc echo "export SINGULARITY_CACHEDIR=/beegfs/work/tu_iioba01/apptainer_cache " >> ~/.bashrc source ~/.bashrc conda activate nf-core
Usage
Install a nf-core pipeline
You could start and run pipelines now and the pipeline will pull all containers themselves. But we experienced problems when a pipeline started more than one job that pulls the same image. Thus we recommend to download the pipeline first using the nf-core tools. In this example we will use the rnaseq pipeline. If you need another pipeline,
nf-core download -x none -d -u amend --container-system singularity -r 3.14.0 rnaseq
nf-core tools can download pipelines and also download Singularity containers.