Merge pull request #802 from jscgh/add-unsw_katana

Add unsw katana

.github/CODEOWNERS

@@ -2,3 +2,4 @@
 **/giga** @MartinGrignard
 **/shu_bmrc** @lquayle88
 **/utd_ganymede** @edmundmiller @alyssa-ab
+**/unsw_katana** @jscgh

.github/workflows/main.yml

@@ -100,6 +100,7 @@ jobs:
           - "janelia"
           - "jax"
           - "jex"
+          - "unsw_katana"
           - "ku_sund_danhead"
           - "leicester"
           - "lugh"

README.md

@@ -152,6 +152,7 @@ Currently documentation is available for the following systems:
 - [Janelia Research Campus](docs/janelia.md)
 - [JAX](docs/jax.md)
 - [Jex](docs/jex.md)
+- [UNSW_Katana](docs/unsw_katana.md)
 - [KU SUND DANHEAD](docs/ku_sund_danhead.md)
 - [LUGH](docs/lugh.md)
 - [M3C](docs/m3c.md)

conf/pipeline/proteinfold/unsw_katana.config

@@ -0,0 +1,21 @@
+profiles {
+    unsw_katana {
+        params {
+            config_profile_contact     = '@jscgh'
+            config_profile_description = 'nf-core/proteinfold UNSW Katana profile provided by nf-core/configs'
+        }
+        process {
+            executor = 'pbspro'
+            queue = 'submission'
+
+            withLabel:gpu_compute {
+                accelerator         = 1
+                clusterOptions      = { "-l host=k095 -l ngpus=1 -l ncpus=${task.cpus} -l mem=${task.memory.toMega()}mb" }
+            }
+
+            withName: 'RUN_HELIXFOLD3' {
+                containerOptions    = "--bind \${TMPDIR}:/tmp,\${PWD} --env CUDA_VISIBLE_DEVICES=0"
+            }
+        }
+    }
+}

conf/unsw_katana.config

@@ -0,0 +1,53 @@
+// UNSW Katana nf-core configuration profile
+
+
+params {
+    config_profile_description = 'UNSW Katana HPC profile provided by nf-core/configs.'
+    config_profile_contact = '@jscgh'
+    config_profile_url = 'https://docs.restech.unsw.edu.au/'
+}
+
+process {
+    executor = 'pbspro'
+    queue = 'submission'
+
+    resourceLimits = [
+    memory: 248.GB,
+    cpus: 24,
+    time: 100.h
+    ]
+
+    withLabel:process_single {
+        cpus   = { 1                       }
+        memory = { 4.GB     * task.attempt }
+        time   = { 2.h      * task.attempt }
+    }
+    withLabel:process_low {
+        cpus   = { 2        * task.attempt }
+        memory = { 12.GB    * task.attempt }
+        time   = { 2.h      * task.attempt }
+    }
+    withLabel:process_medium {
+        cpus   = { 8        * task.attempt }
+        memory = { 62.GB    * task.attempt }
+        time   = { 12.h     * task.attempt }
+    }
+    withLabel:process_high {
+        cpus   = { 12       * task.attempt }
+        memory = { 124.GB    * task.attempt }
+        time   = { 48.h     * task.attempt }
+    }
+    withLabel:process_long {
+        time   = { 100.h     * task.attempt }
+    }
+    withLabel:process_high_memory {
+        memory = { 248.GB   * task.attempt }
+    }
+    withLabel:error_ignore {
+        errorStrategy = 'ignore'
+    }
+    withLabel:error_retry {
+        errorStrategy = 'retry'
+        maxRetries    = 1
+    }
+}

docs/unsw_katana.md

@@ -0,0 +1,31 @@
+# nf-core/configs: USNW Katana HPC Configuration
+
+nf-core pipelines have been successfully configured for use on the [UNSW Katana](https://docs.restech.unsw.edu.au/) at the University of New South Wales, Sydney, Australia.
+
+To run an nf-core pipeline at UNSW Katana, run the pipeline with `-profile singularity,unsw_katana`. This will download and launch the [`unsw_katana.config`](../conf/unsw_katana.config) which has been pre-configured with a setup suitable for the unsw katana HPC cluster. Using this profile, a Singularity image image containing all of the required software will be used for the pipeline.
+
+## Launch an nf-core pipeline on Katana
+
+### Prerequisites
+
+Before running the pipeline you will need to load Nextflow and Java, both of which are globally installed modules on Katana. You can do this by running the commands below:
+
+```bash
+module purge
+module load nextflow java
+```
+
+### Execution command
+
+```bash
+module load nextflow
+module load java
+
+nextflow run <nf-core_pipeline>/main.nf \
+    -profile singularity,unsw_katana \
+    <additional flags>
+```
+
+### Queue limits
+
+This config is defined in line with the [UNSW Katana queue limits](https://docs.restech.unsw.edu.au/using_katana/running_jobs/#job-queue-limits-summary).

nfcore_custom.config

@@ -208,6 +208,9 @@ profiles {
     jex {
         includeConfig "${params.custom_config_base}/conf/jex.config"
     }
+    unsw_katana {
+        includeConfig "${params.custom_config_base}/conf/unsw_katana.config"
+    }
     ku_sund_danhead {
         includeConfig "${params.custom_config_base}/conf/ku_sund_danhead.config"
     }

pipeline/proteinfold.config

@@ -12,4 +12,7 @@ profiles {
     crg {
         includeConfig "${params.custom_config_base}/conf/pipeline/proteinfold/crg.config"
     }
+    unsw_katana {
+        includeConfig "${params.custom_config_base}/conf/pipeline/proteinfold/unsw_katana.config"
+    }
 }