Merge branch 'nf-core:master' into master

.github/workflows/main.yml

@@ -43,6 +43,7 @@ jobs:
           - "cbe"
           - "ccga_dx"
           - "ccga_med"
+          - "cedars"
           - "cfc"
           - "cfc_dev"
           - "cheaha"

README.md

@@ -99,6 +99,7 @@ Currently documentation is available for the following systems:
 - [CBE](docs/cbe.md)
 - [CCGA_DX](docs/ccga_dx.md)
 - [CCGA_MED](docs/ccga_med.md)
+- [Cedars-Sinai](docs/cedars.md)
 - [CFC](docs/cfc.md)
 - [CHEAHA](docs/cheaha.md)
 - [Computerome](docs/computerome.md)

conf/cedars.config

@@ -0,0 +1,26 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Cedars-Sinai Medical Center HPC Profile'
+  config_profile_contact = 'Alex Rajewski (@rajewski)'
+  config_profile_url = 'https://www.cedars-sinai.edu/research/cores/informatics-computing/resources.html'
+  max_memory = 90.GB
+  max_cpus = 10
+  max_time = 240.h
+}
+
+// Specify the queing system
+executor {
+  name = "sge"
+}
+
+process {
+  penv = 'smp'
+  beforeScript =
+  """
+  module load 'singularity/3.6.0'
+  """
+}
+
+singularity {
+  enabled = true
+}

conf/pipeline/eager/eva.config

@@ -69,6 +69,11 @@ process {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
    }
+   
+  withName: fastqc_after_clipping {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
+   }
 
   withName: adapter_removal {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
@@ -261,6 +266,11 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
+        
+        withName: fastqc_after_clipping {
+          clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+        }
 
         withName: adapter_removal {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
@@ -441,6 +451,11 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
           errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
+        
+        withName: fastqc_after_clipping {
+          clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+        }
 
         withName: adapter_removal {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" }

conf/pipeline/sarek/munin.config

@@ -23,7 +23,7 @@ params {
 // Specific nf-core/sarek process configuration
 process {
   withLabel:sentieon {
-    module    = {params.sentieon ? 'sentieon/202112.00' : null}
+    module    = {params.sentieon ? 'sentieon/202112.02' : null}
     container = {params.sentieon ? null : container}
   }
 }

docs/cedars.md

@@ -0,0 +1,7 @@
+# Cedars-Sinai Medical Center HPC
+
+- You will need HPC access from EIS, which can be requested in the Service Center.
+- You will need to load the nextflow module on the HPC before running any pipelines (`module load nextflow`). This should automatically load Java as well.
+- Run this with `-profile cedars`
+- By default this config file does not specify a queue for submission, and things will thus go to `all.q`. Because of that, the memory and cpu limits have been set accordingly.
+- We highly recommend specifying a location of a cache directory to store singularity images (so you re-use them across runs, and not pull each time), by specifying the location with the `$NXF_SINGULARITY_CACHE_DIR` bash environment variable in your `.bash_profile` or `.bashrc`

nfcore_custom.config

@@ -24,6 +24,7 @@ profiles {
   cbe          { includeConfig "${params.custom_config_base}/conf/cbe.config" }
   ccga_dx      { includeConfig "${params.custom_config_base}/conf/ccga_dx.config" }
   ccga_med     { includeConfig "${params.custom_config_base}/conf/ccga_med.config" }
+  cedars       { includeConfig "${params.custom_config_base}/conf/cedars.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
   cheaha       { includeConfig "${params.custom_config_base}/conf/cheaha.config" }