Merge branch 'master' into Sanger-Update

README.md

@@ -62,7 +62,7 @@ If you decide to upload your custom config file to `nf-core/configs` then this w
 You will simply have to specify `-profile <config_name>` in the command used to run the pipeline.
 See [`nf-core/configs`](https://github.com/nf-core/configs/tree/master/conf) for examples.
 
-Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](Using an existing config)), and then continuing with the next steps.
+Before adding your config file to nf-core/configs, we highly recommend writing and testing your own custom config file (as described [above](https://github.com/nf-core/configs#using-an-existing-config)), and then continuing with the next steps.
 
 N.B. In your config file, please also make sure to add an extra `params` section with `params.config_profile_description`, `params.config_profile_contact` and `params.config_profile_url` set to reasonable values.
 Users will get information on who wrote the configuration profile then when executing a nf-core pipeline and can report back if there are things missing for example.

conf/crukmi.config

@@ -12,7 +12,7 @@ singularity {
 }
 
 process {
-  beforeScript = 'module load apps/apptainer/1.2.0'
+  beforeScript = 'module load apps/apptainer'
   executor     = 'slurm'
   queue        = { task.memory <= 240.GB ? 'compute' : 'hmem' }
 

conf/pipeline/taxprofiler/hasta.config

@@ -2,6 +2,7 @@ params {
   // Specific nf-core/configs params
   config_profile_contact = 'Sofia Stamouli (@sofstam)'
   config_profile_description = 'nf-core/taxprofiler HASTA profile provided by nf-core/configs'
+  validationSchemaIgnoreParams = "priority,clusterOptions,schema_ignore_params,genomes,fasta"
 }
 
 process {

conf/vsc_kul_uhasselt.config

@@ -46,7 +46,7 @@ profiles {
             config_profile_description = 'HPC_GENIUS profile for use on the genius cluster of the VSC HPC.'
             config_profile_contact = '[email protected]'
             config_profile_url = 'https://docs.vscentrum.be/en/latest/index.html'
-            max_memory = 720.GB  // 768 - 48 so 48GB for overhead
+            max_memory = 703.GB  // 768 - 65 so 65GB for overhead, max is 720000MB
             max_time = 168.h
             max_cpus = 36
         }
@@ -55,7 +55,7 @@ profiles {
             executor = 'slurm'
             queue = {
                 switch (task.memory) {
-                case { it >=  170.GB }: // 192 - 22
+                case { it >=  175.GB }: // max is 180000
                     switch (task.time) {
                     case { it >= 72.h }:
                         return 'dedicated_big_bigmem'
@@ -81,7 +81,7 @@ profiles {
             config_profile_description = 'HPC_WICE profile for use on the Wice cluster of the VSC HPC.'
             config_profile_contact = '[email protected]'
             config_profile_url = 'https://docs.vscentrum.be/en/latest/index.html'
-            max_memory = 2000.GB // 2048 - 48 so 48GB for overhead
+            max_memory = 1968.GB // max is 2016000
             max_cpus = 72
             max_time = 168.h
         }
@@ -90,7 +90,7 @@ profiles {
             executor = 'slurm'
             queue = {
                 switch (task.memory) {
-                case { it >=  220.GB }:  // 256 - 36
+                case { it >=  239.GB }:  // max is 244800
                     switch (task.time) {
                     case { it >= 72.h }:
                         return 'dedicated_big_bigmem'
@@ -116,7 +116,7 @@ profiles {
             config_profile_description = 'HPC_SUPERDOME profile for use on the genius cluster of the VSC HPC.'
             config_profile_contact = '[email protected]'
             config_profile_url = 'https://docs.vscentrum.be/en/latest/index.html'
-            max_memory = 708.GB // 756 - 48
+            max_memory = 5772.GB // 6000 - 228 so 228GB for overhead, max is 5910888MB
             max_cpus = 14
             max_time = 168.h
         }

docs/crukmi.md

@@ -2,14 +2,14 @@
 
 All nf-core pipelines have been successfully configured for the use on the HPC (griffin) at Cancer Research UK Manchester Institute.
 
-To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/crukmi.config) which has been pre-configured with a setup suitable for the griffin HPC. Using this profile, singularity images will be downloaded to run on the cluster and stored in a centralised location.
+To use, run the pipeline with `-profile crukmi`. This will download and launch the [`crukmi.config`](../conf/crukmi.config) which has been pre-configured with a setup suitable for the Griffin HPC. Using this profile, Apptainer/Singularity images will be downloaded to run on the cluster and stored in a centralised location.
 
 Before running the pipeline you will need to load Nextflow using the environment module system, for example via:
 
 ```bash
 ## Load Nextflow environment modules
 module purge
-module load apps/nextflow/22.04.5
+module load apps/nextflow
 ```
 
 The pipeline should always be executed inside a workspace on the `/scratch/` system. All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large.

pipeline/methylseq.config

@@ -0,0 +1,9 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/methylseq custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/methylseq folder and imported
+ * under a profile name here.
+ */