Merge branch 'nf-core:master' into master

.github/workflows/main.yml

@@ -41,6 +41,7 @@ jobs:
             - 'genouest'
             - 'gis'
             - 'google'
+            - 'hasta'
             - 'hebbe'
             - 'icr_davros'
             - 'ifb_core'
@@ -71,6 +72,6 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - name: Check ${{ matrix.profile }} profile
         env:
-          SCRATCH: '~'
+          SCRATCH: "~"
           NXF_GLOBAL_CONFIG: awsbatch.config
         run: nextflow run ${GITHUB_WORKSPACE}/configtest.nf --custom_config_base=${GITHUB_WORKSPACE} -profile ${{ matrix.profile }}

README.md

@@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
 * [GENOUEST](docs/genouest.md)
 * [GIS](docs/gis.md)
 * [GOOGLE](docs/google.md)
+* [HASTA](docs/hasta.md)
 * [HEBBE](docs/hebbe.md)
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)

conf/hasta.config

@@ -0,0 +1,40 @@
+// Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Hasta, a local cluster setup at Clinical Genomics, Stockholm.'
+  config_profile_contact = 'Clinical Genomics, Stockholm'
+  config_profile_url = 'https://github.com/Clinical-Genomics'
+  priority = null
+  clusterOptions = null
+  schema_ignore_params = "priority,clusterOptions"
+}
+
+singularity {
+  enabled = true
+}
+
+params {
+    max_memory = 180.GB
+    max_cpus   = 36
+    max_time   = 336.h    
+}
+
+process {
+    executor = 'slurm'
+    clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" }    
+}
+
+profiles {
+    dev_prio {
+        params {
+           priority = 'development'
+           clusterOptions = "--qos=low"
+        }
+    }
+
+    prod_prio {
+        params {
+            priority = 'production'
+            clusterOptions = "--qos=low"
+        }
+    }
+}

conf/pipeline/raredisease/hasta.config

@@ -0,0 +1,11 @@
+process {
+    
+    withName:'PICARD_MARKDUPLICATES' {
+        cpus   = { check_max( 13      * task.attempt, 'cpus' ) }
+        memory = { check_max( 130.GB  * task.attempt, 'memory' ) }
+    }
+    withName:'DEEPVARIANT' {
+        cpus   = { check_max( 16      * task.attempt, 'cpus' ) }
+        memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
+    }
+}

docs/hasta.md

@@ -0,0 +1,16 @@
+# nf-core/configs: Hasta Configuration
+
+## Using the Hasta config profile
+
+Before running the pipeline `Nextflow` will need to be install in the conda environment being used.
+
+To use, run the pipeline with `-profile hasta` (one hyphen).
+This will download and launch the [`hasta.config`](../conf/hasta.config) which has been pre-configured with a setup suitable for the hasta servers.
+It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
+Using this profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline.
+
+Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. A use case: `NXF_SINGULARITY_CACHEDIR=/path/to/images; export NXF_SINGULARITY_CACHEDIR` before running the pipeline.
+
+## Development and production config
+
+Each user on hasta has a priority based on their allocated team, either development or production. To enable this when submitting a job to Slurm, submit with `-profile hasta,dev_prio` or `-profile hasta,prod_prio`. This overwrites certain parts of the config and submits the job based on different priorities.

nfcore_custom.config

@@ -35,6 +35,7 @@ profiles {
   genouest     { includeConfig "${params.custom_config_base}/conf/genouest.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   google       { includeConfig "${params.custom_config_base}/conf/google.config" }
+  hasta        { includeConfig "${params.custom_config_base}/conf/hasta.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }

pipeline/raredisease.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/raredisease custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/raredisease folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/raredisease/hasta.config" }  
+}