uondrs_ada config file : WIP

.github/workflows/main.yml

@@ -34,6 +34,7 @@ jobs:
     strategy:
       matrix:
         profile:
+          - "uondrs_ada"
           - "abims"
           - "adcra"
           - "alice"

README.md

@@ -296,6 +296,9 @@ Currently documentation is available for the following pipeline:
 
 - viralrecon
   - [genomes](docs/pipeline/viralrecon/genomes.md)
+
+- rnaseq
+   - [uondrs_ada](docs/pipeline/rnaseq/uondrs_ada.md)
 
 ### Enabling pipeline-specific configs within a pipeline
 

conf/uondrs_ada.config

@@ -0,0 +1,55 @@
+//Profile config names for nf-core/configs
+
+params {
+    // Config Params
+    config_profile_description = 'University of Nottingham DRS - HPC Profile -- provided by nf-core/configs.'
+    config_profile_contact = 'Niraj Shah (@ShahNiraj)'
+    config_profile_url = 'https://forms.office.com/Pages/ResponsePage.aspx?id=7qe9Z4D970GskTWEGCkKHpYhN2mnMuNPm5Y3GQx5rlxUMzJQTDE0OUVSNUtHT0UyU0o2UTRCQzNaQSQlQCN0PWcu'
+
+}
+
+// definition of the slurm executor. Run the pipeline in a node able to submit jobs to a HPC via sbatch
+singularity {
+  enabled = true
+  autoMounts = true
+  // Some processes don't respect the TMP environment variables: https://github.com/nf-core/rnaseq/issues/115
+}
+
+process {
+  // Global process config
+  executor = 'slurm'
+  queueSize = 10
+  queue = 'defq'
+  submitRateLimit = '10/2min'
+}
+
+process {
+
+    // resources for default process execution
+withLabel:process_low {
+    cpus =  2
+    memory = 12.GB
+    time = 6.h
+  }
+  withLabel:process_medium {
+    cpus = 6
+    memory = 36.GB
+    time = 6.h
+  }
+  withLabel:process_high {
+    cpus = 12
+    memory = 240.GB
+    time = 6.h
+  }
+  withLabel:process_long {
+    time = 20.h
+  }
+  withLabel:error_ignore {
+    errorStrategy = 'ignore'
+  }
+  withLabel:error_retry {
+    errorStrategy = 'retry'
+    maxRetries = 2
+  }
+       // resources for execution of processes / modules with the label "two cpus". This override the default ones.
+}

docs/uondrs_ada.md

@@ -0,0 +1,29 @@
+# nf-core/configs: Ada HPC Configuration
+
+nfcore pipeline rnaseq have been tested on the Ada HPC.
+
+## Before running the pipeline
+
+- You will need an account to use the Ada HPC cluster in order to run the pipeline.
+- Make sure that Singularity and Nextflow are installed.
+- Downlode pipeline singularity images to a HPC system using [nf-core tools](https://nf-co.re/tools/#downloading-pipelines-for-offline-use)
+
+```
+$ conda install nf-core
+$ nf-core download
+```
+
+
+
+
+## Running the pipeline using the adcra config profile
+
+- Run the pipeline within a [screen](https://linuxize.com/post/how-to-use-linux-screen/) or [tmux](https://linuxize.com/post/getting-started-with-tmux/) session.
+- Specify the config profile with `-profile uondrs_ada`.
+
+```
+nextflow run /path/to/nf-core/rnaseq -profile uondrs_ada \
+--genome GRCh38 \
+--igenomes_base /path/to/genome_references/ \
+... # the rest of pipeline flags
+```

nfcore_custom.config

@@ -10,6 +10,7 @@
 
 //Please use a new line per include Config section to allow easier linting/parsing. Thank you.
 profiles {
+    uondrs_ada         { includeConfig "${params.custom_config_base}/conf/uondrs_ada.config" }
     abims              { includeConfig "${params.custom_config_base}/conf/abims.config" }
     adcra              { includeConfig "${params.custom_config_base}/conf/adcra.config" }
     alice              { includeConfig "${params.custom_config_base}/conf/alice.config" }