Merge branch 'master' into kul_gpu

.github/workflows/main.yml

@@ -102,6 +102,7 @@ jobs:
           - "jex"
           - "unsw_katana"
           - "ku_sund_danhead"
+          - "kaust"
           - "leicester"
           - "lugh"
           - "m3c"
@@ -171,7 +172,11 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
-      - name: Install Nextflow
+      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # v4
+        with:
+          distribution: "temurin"
+          java-version: "17"
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "latest-everything"

README.md

@@ -154,6 +154,7 @@ Currently documentation is available for the following systems:
 - [Jex](docs/jex.md)
 - [UNSW_Katana](docs/unsw_katana.md)
 - [KU SUND DANHEAD](docs/ku_sund_danhead.md)
+- [KAUST](docs/kaust.md)
 - [LUGH](docs/lugh.md)
 - [M3C](docs/m3c.md)
 - [MAESTRO](docs/maestro.md)

conf/daisybio.config

@@ -11,7 +11,17 @@ params {
 // define workDir in /nfs/scratch/nf-core_work/ named after the launch dir
 def work_dir = "/nfs/scratch/nf-core_work/"
 if(new File(work_dir).exists() && System.getenv("PWD")) {
-        workDir = work_dir+System.getenv("PWD").tokenize('/').join('.')
+    work_dir = work_dir+System.getenv("PWD").tokenize('/').join('.')
+    workDir = work_dir
+
+    // if directory does not exist, create it and set the group to the group launch dir
+    if(!new File(work_dir).exists()) {
+        "mkdir -p ${work_dir}".execute()
+        def pwd = System.getenv("PWD")
+        def group = "stat -c %g ${pwd}".execute().text.trim()
+        "chgrp -R ${group} ${work_dir}".execute()
+        "chmod -R g+s ${work_dir}".execute()
+    }
 }
 
 process {

conf/kaust.config

@@ -0,0 +1,67 @@
+// KAUST Config Profile
+params {
+    config_profile_name = 'KAUST'
+    config_profile_description = 'Profile for use on King Abdullah Univesity of Science and Technology (KAUST) Ibex Cluster.'
+    config_profile_contact = 'Husen Umer (@kaust.edu.sa)'
+    config_profile_url = 'https://docs.hpc.kaust.edu.sa/quickstart/ibex.html'
+    save_reference = false
+    igenomes_ignore = true
+}
+
+// Load genome resources and assets hosted by the Bioinformatics team on IBEX cluster
+// includeConfig '/biocorelab/BIX/resources/configs/genomes.yaml'
+
+singularity {
+    enabled = true
+    autoMounts = true
+    pullTimeout = '60 min'
+    // Use existing images from the centralized library, if available
+    libraryDir = "/biocorelab/BIX/resources/singularity/images/"
+    // Download images that are missing from the library to user space
+    cacheDir = "/home/$USER/.singularity/nf_images/"
+}
+
+process {
+    executor = 'slurm'
+    clusterOptions = "-p batch"
+    maxRetries = 5
+    errorStrategy = { task.exitStatus in [143,137,104,134,139,151,140,247,12] ? 'retry' : 'finish' }
+    beforeScript = 'module load singularity'
+    // Max allowed resources per process on Ibex
+    resourceLimits = [
+        memory: 1600.GB,
+        cpus: 200,
+        time: 10.d
+    ]
+}
+
+process {
+
+    withLabel:process_single {
+        time = 20.h
+    }
+
+    withLabel:process_low {
+        cpus   = { 4 * task.attempt }
+        memory = { 16.GB * task.attempt }
+        time   = { 6.h  * task.attempt }
+    }
+
+    withLabel:process_medium {
+        cpus   = { 20 * task.attempt }
+        memory = { 96.GB * task.attempt }
+        time   = { 12.h  * task.attempt }
+    }
+
+    withLabel:process_high {
+        cpus   = { 40 * task.attempt }
+        memory = { 256.GB * task.attempt }
+        time   = { 20.h  * task.attempt }
+    }
+
+    withLabel:process_long {
+        cpus   = { 12 * task.attempt }
+        memory = { 128.GB * task.attempt }
+        time   = { 96.h  * task.attempt }
+    }
+}

docs/kaust.md

@@ -0,0 +1,43 @@
+# nf-core/configs: KAUST Configuration
+
+manage the pipeline jobs via the nf-core/configs: KAUST Configuration
+
+The purpose of this custom configurations is to streamline executing nf-core pipelines on the KAUST Ibex cluster.
+
+## Getting help
+
+We have a wiki page dedicated to the Bioinformatics team at KAUST to help users: [Bioinformatics Workflows](https://bclwiki.kaust.edu.sa/en/bix/analysis/public/bioinformatics-workflows).
+
+## Using the KAUST config profile
+
+The recommended way to activate `Nextflow`, that is needed to run the `nf-core` workflows on Ibex,
+is to use the [module system](https://docs.hpc.kaust.edu.sa/soft_env/prog_env/modulesystem/basic_commands.html):
+
+```bash
+# Log in to the desired cluster
+ssh <USER>@ilogin.kaust.edu.sa
+
+# Activate the modules, you can also choose to use a specific version with e.g. `Nextflow/24.04.4`.
+module load nextflow
+```
+
+Launch the pipeline with `-profile kaust` (one hyphen) to run the workflows using the KAUST profile.
+This will download and launch the [`kaust.config`](../conf/kaust.config) which has been pre-configured with a setup suitable for the KAUST servers.
+It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler and `Singularity` to run the tasks.
+Using the KAUST profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline. To avoid downloading same images by multiple users, we provide a singularity `libraryDir` that is configured to use images already downloaded in our central container library. Images missing from our library will be downloaded to your home directory path as defined by `cacheDir`.
+
+The KAUST profile makes running the nf-core workflows as simple as:
+
+```bash
+
+module load nextflow
+module load singularity
+
+# Launch nf-core pipeline with the kaust profile, e.g. for analyzing human data:
+$ nextflow run nf-core/<PIPELINE> -profile kaust -r <PIPELINE_VERSION> --genome GRCh38.p14 --samplesheet input.csv [...]
+```
+
+Where `input_csv` contains information about the samples and datafile paths.
+
+Remember to use `-bg` to launch `Nextflow` in the background, so that the pipeline doesn't exit if you leave your terminal session.
+Alternatively, you can also launch `Nextflow` in a `tmux` or a `screen` session.

nfcore_custom.config

@@ -214,6 +214,9 @@ profiles {
     ku_sund_danhead {
         includeConfig "${params.custom_config_base}/conf/ku_sund_danhead.config"
     }
+    kaust {
+        includeConfig "${params.custom_config_base}/conf/kaust.config"
+    }
     leicester {
         includeConfig "${params.custom_config_base}/conf/leicester.config"
     }

pipeline/tumourevo.config

@@ -0,0 +1,12 @@
+/*
+* -------------------------------------------------
+*  nfcore/tumourevo custom profile Nextflow config file
+* -------------------------------------------------
+* Config options for custom environments.
+* Cluster-specific config options should be saved
+* in the conf/pipeline/tumourevo folder and imported
+* under a profile name here.
+*/
+
+profiles {
+}