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howto:bioinformatics [2025/05/06 11:03]
nmfuphi [Singularity] 		howto:bioinformatics [2025/05/21 10:50] (current)
nmfuphi [Singularity]
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 === Shared Conda Environments === === Shared Conda Environments ===
  
-For most use cases — especially in bioinformatics — CHPC provides pre-built, **shared Conda environments** installed under:+For most use cases, especially in bioinformatics, CHPC provides pre-built, **shared Conda environments** installed under:
  
   '/apps/chpc/bio/anaconda3-2020.02/envs'   '/apps/chpc/bio/anaconda3-2020.02/envs'
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 module load conda_init module load conda_init
 </code> </code>
 +
 +The second module updates your .bashrc file by adding necessary shell variables.
 +To apply these changes, you can either log out and log back in, or run: <code bash>source ~/.bashrc. </code>
 +After this setup, you won’t need to load additional modules for your jobs—only the eval and conda activate steps are required.
  
 === Step 2: Initialize Conda in your shell === === Step 2: Initialize Conda in your shell ===
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 If you need software that is not included in the shared environments, you may create your own **private Conda environment**. This gives you full control over the software stack and package versions. If you need software that is not included in the shared environments, you may create your own **private Conda environment**. This gives you full control over the software stack and package versions.
  
-> **Important:** Do **not** install environments in your home directory (''/home/<username>'') — use your Lustre project storage instead.+> **Important:** Do **not** install environments in your home directory (''/home/<username>'') -use your Lustre project storage instead.
  
 === Step-by-step setup === === Step-by-step setup ===
 +ssh to username@scp.chpc.ac.za, the password is the same as the one you use on lengau
 === Step 1: Load Conda === === Step 1: Load Conda ===
 <code bash> <code bash>
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   * ✅ Use **shared environments** whenever possible for consistency and faster setup.   * ✅ Use **shared environments** whenever possible for consistency and faster setup.
   * 📁 Create private environments **only in Lustre** directories, such as ''/mnt/lustre/<username>''.   * 📁 Create private environments **only in Lustre** directories, such as ''/mnt/lustre/<username>''.
-  * ⚠️ Do **not** use Conda in your ''$HOME'' directory — it may lead to quota issues or slow performance.+  * ⚠️ Do **not** use Conda in your ''$HOME'' directory, it may lead to quota issues or slow performance.
   * 📌 Use the ''--prefix'' flag to create environments with absolute paths, especially on clusters where ''--name'' may default to ''$HOME''.   * 📌 Use the ''--prefix'' flag to create environments with absolute paths, especially on clusters where ''--name'' may default to ''$HOME''.
   * 🧼 Periodically clean up unused environments with `conda remove --all`.   * 🧼 Periodically clean up unused environments with `conda remove --all`.
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 #PBS -N singularity_job #PBS -N singularity_job
 #PBS -q normal #PBS -q normal
-#PBS -l select=1:ncpus=8:mem=32gb+#PBS -l select=1:ncpus=24
 #PBS -l walltime=12:00:00 #PBS -l walltime=12:00:00
 #PBS -o singularity_output.log #PBS -o singularity_output.log
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 </code> </code>
  
 +==== Nextflow ====
  
-**Need Help?**+Nextflow is a free and open-source workflow management system that enables the development and execution of data analysis pipelines. It simplifies complex computational workflows and ensures reproducibility, scalability, and portability—whether you’re working on a laptop, HPC cluster, or in the cloud. Nextflow workflows are written using DSL2, allowing modular code design and seamless integration with container technologies like Docker, Singularity, Conda, or manual installations. 
 +[[https://www.nextflow.io/docs/latest/index.html|Official documentation is available here]].
  
-Submit a ticket:+=== Running Nextflow on the CHPC Cluster ===
  
-👉 https://users.chpc.ac.za/helpdesk/tickets/submit/+CHPC supports Nextflow workflows through Singularity containers. Since compute nodes have no internet access, all dependencies must be downloaded in advance on the login node.
  
-**Include:**+=== 1. Connect to the Login Node === 
 + 
 +Log into the CHPC login node using your Lengau credentials: 
 + 
 +<code bash> ssh username@scp.chpc.ac.za </code> 
 + 
 +Use this session to prepare your workflow and submit jobs. 
 + 
 +=== 2. Load the Nextflow Module === 
 + 
 +Load the necessary environment modules: 
 + 
 +<code bash>module load chpc/BIOMODULES nextflow 
 +module load chpc/singularity 
 +</code> 
 + 
 +Note: Modules must be reloaded in every new session unless added to your ~/.bashrc. 
 + 
 +=== 3. Pull Workflow and Dependencies === 
 + 
 +Pull your workflow and dependencies on the login1 node: 
 + 
 +Pull the workflow: 
 +<code bash> nextflow pull nf-core/rnaseq </code> 
 + 
 +Run a test execution: 
 +<code bash> nextflow run nf-core/rnaseq -profile test </code> 
 + 
 +This will: 
 + 
 +Cache the workflow in ~/.nextflow/assets/ 
 + 
 +Download containers (if configured) 
 + 
 +Retrieve auxiliary files and dependencies 
 + 
 +=== Cached Files and Workflow Structure === 
 + 
 +Workflow code is stored in: 
 +<code>~/.nextflow/assets</code> 
 + 
 +Container images are stored in: 
 +<code>~/.singularity</code> 
 + 
 +**🗂 Finding the nextflow.config File** 
 + 
 +After pulling a workflow, you’ll typically find the nextflow.config file in its root directory. 
 + 
 +Example: 
 +<code bash> 
 +cd ~/.nextflow/assets/nf-core/rnaseq/ 
 +ls 
 +</code> 
 + 
 +Look for: 
 +<code>nextflow.config</code> 
 +If missing, config files may reside in the conf/ directory or be fetched remotely. You can always override settings by creating your own nextflow.config. 
 + 
 +🚫 No Manual PBS Scripts Needed 
 +Nextflow automatically generates and submits PBS scripts. You only define resources in nextflow.config. 
 + 
 +=== ⚙️ Configuration with nextflow.config === 
 + 
 +== 🔧 1. Global Resource Settings == 
 + 
 +Set default resource usage for all workflow processes: 
 + 
 +<code nextflow> process { 
 +    executor = 'pbs' 
 + 
 +    withLabel: big_job { 
 +        queue = 'smp' 
 +        cpus = 24 
 +        memory = '120 GB' 
 +        time = '24h' 
 +    } 
 +} 
 + </code> 
 +== 🏷️ 2. Custom Resource Labels == 
 + 
 +Customize resources for specific process groups using labels: 
 + 
 +<code nextflow> 
 +process { 
 +    executor = 'pbs' 
 + 
 +    withLabel: big_job { 
 +        cpus = 16 
 +        memory = '64 GB' 
 +        time = '12h' 
 +        queue = 'smp' 
 +    } 
 + 
 +    withLabel: short_job { 
 +        cpus = 1 
 +        memory = '1 GB' 
 +        time = '15m' 
 +        queue = 'smp' 
 +    } 
 +} 
 + 
 +</code> 
 + 
 +Use the label in your pipeline: 
 +<code nextflow> 
 +process bigTask { 
 +label 'big_job' 
 +... 
 +} 
 +</code> 
 + 
 +== 📦 3. Singularity Integration == 
 + 
 +Enable Singularity support: 
 + 
 +<code nextflow> singularity.enabled = true  
 +singularity.autoMounts = true </code> 
 + 
 +Specify containers: 
 + 
 +From Docker Hub: 
 +<code nextflow> 
 +process.container = 'docker://biocontainers/fastqc:v0.11.9_cv8' 
 +</code>     
 +From local image: 
 +<code nextflow> 
 +process.container = '/path/to/image.sif' 
 +</code> 
 + 
 +Set cache directory to avoid re-downloads: 
 + 
 +<code nextflow> singularity.cacheDir = '/path/to/.singularity' </code> 
 +== 🖥️ 4. PBS Executor Settings == 
 + 
 +Customize PBS job submission: 
 + 
 + 
 +<code nextflow>  
 +executor { 
 +  name = 'pbs' 
 +  queueSize = 20 
 +  submitOptions = '-V -m abe -M your@email.com' 
 +}  
 +</code> 
 + 
 +== 📂 5. Using Profiles == 
 + 
 +Profiles let you switch configurations easily: 
 + 
 +<code nextflow> profiles { 
 +  standard { 
 +    process.executor = 'pbs' 
 +    process.queue = 'smp' 
 +  } 
 + 
 +  local { 
 +    process.executor = 'local' 
 +    docker.enabled = false 
 +  } 
 + 
 +  cluster_singularity { 
 +    process.executor = 'pbs' 
 +    singularity.enabled = true 
 +    process.container = 'file:///path/to/container.sif' 
 +  } 
 +} 
 + </code> 
 +Run a profile: 
 + 
 +<code bash> nextflow run main.nf -profile cluster_singularity </code> 
 + 
 +== 🚫 Offline Mode == 
 + 
 +Run jobs on compute nodes without internet access: 
 + 
 +<code bash> nextflow run ~/.nextflow/assets/nf-core/rnaseq \  
 +-profile singularity -offline </code> 
 +⚠️ Always include -offline on compute nodes to prevent online fetching. 
 + 
 +=== 🧭 Debugging and Logs === 
 + 
 +Each Nextflow process generates a unique work directory (work/ab/xyz123), containing: 
 + 
 +.command.run — generated PBS job script 
 + 
 +.command.sh — wrapped shell script 
 + 
 +.command.log — job output 
 + 
 +.exitcode — exit status 
 + 
 +To inspect a failed job: 
 + 
 +<code bash> cd work/ab/xyz123/ 
 +less .command.log </code> 
 + 
 +=== ✅ Summary === 
 + 
 +nextflow.config centralizes all pipeline settings. 
 + 
 +No need to write PBS scripts manually. 
 + 
 +Resources, container usage, and submission options are all configurable. 
 + 
 +Profiles improve portability and reproducibility. 
 + 
 +Offline mode is essential for CHPC compute node compatibility. 
 + 
 +🧠 Tip: For workflows requiring reference data, bind directories just like with containers: 
 + 
 +<code bash> nextflow run /path/to/my_pipeline -profile singularity -offline \  
 +--input /data/input.fastq \  
 +--genomeDir /mnt/lustre/bsp/DB/genomes 
 +</code> 
 + 
 +🧹 Clean Up: 
 +Nextflow stores all its cache files in your home directory, so it's important to clean up these files once you're finished using a workflow to avoid running out of space. 
 +<code bash> 
 +rm -rf ~/.nextflow/assets/  
 +rm -rf ~/.nextflow/tmp  
 +rm -rf ~/.singularity 
 +</code>
  
-The commands you ran, singularity image used, paths and error logs+=== Need Help? === 
 +If you encounter issues or need a specific tool installed contact the CHPC support team at: 
 +  * 📧 help@chpc.ac.za 
 +  * https://users.chpc.ac.za/helpdesk/tickets/submit/ 
 +Include your job script and all errors encountered.
 ===== Basic examples ===== ===== Basic examples =====
  
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