Merge pull request #1086 from nf-core/deprecate_wustl_htcf

FIX: Restore config + add warning

Author: jfy133

.github/workflows/main.yml

@@ -214,6 +214,7 @@ jobs:
           - "vsc_kul_uhasselt"
           - "vsc_ugent"
           - "wehi"
+          - "wustl_htcf"
           - "xanadu"
           - "york_viking"
 

conf/wustl_htcf.config

@@ -0,0 +1,52 @@
+// Forked from https://github.com/nf-core/configs/blob/master/conf/prince.config
+
+params {
+    config_profile_description  = """
+    WUSTL High Throughput Computing Facility cluster profile provided by nf-core/configs.
+    Run from your scratch directory, the output files may be large!
+    Please consider running the pipeline on a compute node the first time, as it will be pulling the docker image, which will be converted into a singularity image, which is heavy on the login node. Subsequent runs can be done on the login node, as the docker image will only be pulled and converted once. By default, the images will be stored in ${params.singularityDir}
+    """.stripIndent()
+    config_profile_contact      = "Gavin John <gavinjohn@wustl.edu>"
+    config_profile_url          = "https://github.com/nf-core/configs/blob/master/docs/wustl_htcf.md"
+
+    max_cpus = 24
+    max_memory = 750.GB
+    max_time = 168.h
+
+    // Define singularity directory based on LAB environment variable or group membership
+    singularityDir = "/ref/${System.getenv("LAB") ?: "id -nG".execute().text.split(" ").last().trim()}/data/singularity_images_nextflow"
+
+    warning_message = {
+        System.out.println("WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+        System.out.println("WARNING:")
+        System.out.println("WARNING: THIS CONFIG IS NO LONGER MAINTAINED.")
+        System.out.println("WARNING:")
+        System.out.println("WARNING: THIS CONFIG WILL BE DEPRECATED BY THE END OF MAY 2026 DUE TO AN UPCOMING VERSION NEXTFLOW THAT WILL NOT BE BACKWARDS COMPATIBLE.
+        System.out.println("WARNING: MODIFICATIONS TO THIS CONFIG AND TESTING BY USERS OF THE INFRASTRUCTURE ARE REQUIRED TO ENSURE THE CONFIG REMAINS FUNCTIONAL.")
+        System.out.println("WARNING:")
+        System.out.println("WARNING: PLEASE GET IN CONTACT WITH THE NF-CORE COMMUNITY VIA SLACK  (#configs CHANNEL) OR EMAIL (https://nf-co.re/join) ASAP")
+        System.out.println("WARNING: TO ALLOW CONTINUED USE OF YOUR CONFIG WITH NF-CORE PIPELINES")
+        System.out.println("WARNING:")
+        System.out.println("WARNING: !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
+    }.call()
+}
+
+spack {
+    enabled = true
+}
+
+singularity {
+    enabled  = true
+    cacheDir = params.singularityDir
+}
+
+process {
+    resourceLimits = [
+        memory: 750.GB,
+        cpus: 24,
+        time: 168.h
+    ]
+    beforeScript = "exec \$( spack load --sh singularity )"
+    executor     = "slurm"
+}
+

docs/wustl_htcf.md

@@ -0,0 +1,25 @@
+# nf-core/configs: WUSTL High Throughput Computing Facility Configuration
+
+Forked from the prince configuration.
+
+<!-- https://github.com/nf-core/configs/blob/master/docs/prince.md -->
+
+## nf-core pipelines that use this repo
+
+All nf-core pipelines that use this config repo (which is most), can be run on the HTCF. **Before** running a pipeline for the first time, go into an interactive slurm session on a compute node (`srun --pty --time=02:00:00 -c 2`), as the docker images for the pipeline will need to be pulled and converted.
+
+Now, run the pipeline of your choice with `-profile wustl_htcf`. This will download and launch `wustl_htcf.config` which has been pre-configured with a setup suitable for the HTCF cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a singularity image before execution of the pipeline. This step **takes time**!!
+An example commandline:
+
+```bash
+nextflow run nf-core/<pipeline name> -profile wustl_htcf <additional flags>
+```
+
+## nf-core pipelines that do not use this repo
+
+If the pipeline has not yet been configured to use the nf-core/configs repository, then you will have to do it manually. Add the following lines to the end of the pipeline's `nextflow.config`
+
+```bash
+// Allow the use of nf-core/configs configuration files
+includeConfig "https://raw.githubusercontent.com/nf-core/configs/master/nfcore_custom.config"
+```

nfcore_custom.config

@@ -466,6 +466,9 @@ profiles {
     wehi {
         includeConfig "${params.custom_config_base}/conf/wehi.config"
     }
+    wustl_htcf {
+        includeConfig "${params.custom_config_base}/conf/wustl_htcf.config"
+    }
     xanadu {
         includeConfig "${params.custom_config_base}/conf/xanadu.config"
     }