Merge branch 'master' into add_snic_tmp

.github/workflows/main.yml

@@ -49,6 +49,7 @@ jobs:
             - 'imperial_mb'
             - 'jax'
             - 'lugh'
+            - 'maestro'
             - 'mpcdf'
             - 'munin'
             - 'nu_genomics'

README.md

@@ -118,6 +118,7 @@ Currently documentation is available for the following systems:
 * [ICR_DAVROS](docs/icr_davros.md)
 * [JAX](docs/jax.md)
 * [LUGH](docs/lugh.md)
+* [MAESTRO](docs/maestro.md)
 * [MPCDF](docs/mpcdf.md)
 * [MUNIN](docs/munin.md)
 * [NU_GENOMICS](docs/nu_genomics.md)

conf/maestro.config

@@ -0,0 +1,49 @@
+params {
+  config_profile_description = 'Institut Pasteur Maestro cluster profile'
+  config_profile_url = 'https://research.pasteur.fr/en/equipment/maestro-compute-cluster/'
+  config_profile_contact = 'Pierre Luisi (@pierrespc)'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '--home $HOME:/home/$USER --bind /pasteur'
+}
+
+profiles {
+    
+    normal {
+        process {
+              executor = 'slurm'
+              scratch = false
+              queue = 'common'
+              clusterOptions = '--qos=normal'
+        }
+
+        params {
+            igenomes_ignore = true
+            igenomesIgnore = true
+            max_memory = 400.GB
+            max_cpus = 96
+            max_time = 24.h
+        }
+    }
+
+    long {
+        process {
+              executor = 'slurm'
+              scratch = false
+              queue = 'common'
+              clusterOptions = '--qos=long'
+        }
+
+        params {
+            igenomes_ignore = true
+            igenomesIgnore = true
+            max_memory = 400.GB
+            max_cpus = 5
+            max_time = 8760.h
+        }
+    }
+
+}

conf/pipeline/eager/maestro.config

@@ -0,0 +1,116 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running nf-core eager on whole genome data or mitogenomes 
+ * -------------------------------------------------
+ * nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear, mitocondrial or unlimitedtime)
+ */
+
+params {
+
+   config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
+
+   config_profile_description = "Simple profiles for assessing computational ressources that fit human nuclear dna, human mitogenomes processing. unlimitedtime is also available "
+
+}
+
+
+profiles {
+
+   nuclear {
+      process {
+         errorStrategy = 'retry'
+         maxRetries = 2
+
+         withName:'makeBWAIndex'{
+            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+            time = { check_max( 12.h * task.attempt, 'time' ) }
+         }
+         withName:'adapter_removal'{
+            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+            time = { check_max( 12.h * task.attempt, 'time' ) }
+         }
+         withName:'bwa'{
+            cpus = { check_max( 40 * task.attempt, 'cpus' ) }
+            memory = { check_max( 40.GB * task.attempt, 'memory' ) }
+            time = 24.h 
+            cache = 'deep'
+         }
+         withName:'markduplicates'{
+            errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+            cpus = { check_max( 16 * task.attempt, 'cpus' ) }
+            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+            time = { check_max( 12.h * task.attempt, 'time' ) }
+         }
+         withName:'damageprofiler'{
+            cpus = 1
+            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+            time = { check_max( 6.h * task.attempt, 'time' ) }
+         }
+         withName:'fastp'{
+            cpus = 8 
+            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+            time = { check_max( 6.h * task.attempt, 'time' ) }
+         }
+         withName:'fastqc'{
+            cpus = 2
+            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+            time = { check_max( 6.h * task.attempt, 'time' ) }
+         }
+      }
+   }
+
+   mitocondrial {
+      process {
+         errorStrategy = 'retry'
+         maxRetries = 2
+
+         withName:'makeBWAIndex'{
+            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+            time = { check_max( 12.h * task.attempt, 'time' ) }
+         }
+         withName:'adapter_removal'{
+            cpus = { check_max( 8 * task.attempt, 'cpus' ) }
+            memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+            time = { check_max( 12.h * task.attempt, 'time' ) }
+         }
+         withName:'bwa'{
+            cpus = { check_max( 5 * task.attempt, 'cpus' ) }
+            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+            time = 24.h 
+         }
+         withName:'markduplicates'{
+            errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
+            cpus = { check_max( 5 * task.attempt, 'cpus' ) }
+            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+            time = { check_max( 6.h * task.attempt, 'time' ) }
+         }
+         withName:'damageprofiler'{
+            cpus = 1
+            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+            time = { check_max( 3.h * task.attempt, 'time' ) }
+         }
+         withName:'fastp'{
+            cpus = 8 
+            memory = { check_max( 5.GB * task.attempt, 'memory' ) }
+            time = { check_max( 3.h * task.attempt, 'time' ) }
+         }
+         withName:'fastqc'{
+            cpus = 2
+            memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+            time = { check_max( 6.h * task.attempt, 'time' ) }
+         }
+      }
+   }
+   unlimitedtime {
+     process {
+        errorStrategy = 'finish'
+
+        cpus = 5
+        memory = 200.GB
+        time = 8760.h
+
+    }
+}

conf/uppmax.config

@@ -13,9 +13,43 @@ singularity {
   envWhitelist = 'SNIC_TMP'
 }
 
+def hostname = "r1"
+try {
+    hostname = "sinfo --local -N -h | grep -F -v CLUSTER: | head -1 | cut -f1 -d' ' ".execute().text.trim()
+} catch (java.io.IOException e) {
+    System.err.println("WARNING: Could not run sinfo to determine current cluster, defaulting to rackham")
+}
+
+// closure to create a suitable clusterOptions
+def clusterOptionsCreator = { m ->
+    String base = "-A $params.project ${params.clusterOptions ?: ''}"
+    // Do not use -p node on irma or if a thin node/core is enough
+    if (m < 125.GB || hostname ==~ "i.*") {
+        return base
+    }
+
+    if (m < 250.GB) {
+        return base + " -p node -C mem256GB "
+    }
+
+
+    // Use mem1TB for remaining cases on rackham (no 512 Gbyte nodes)
+    if (hostname ==~ "r.*") {
+        return base + " -p node -C mem1TB "
+    }
+
+    if (m > 500.GB) {
+       // Special case for snowy very fat node (only remaining case that's above 500 GB)
+       return base + " -p veryfat "
+    }
+
+    // Should only be cases for mem512GB left (snowy and bianca)
+    return base + " -p node -C mem512GB "
+}
+
 process {
   executor = 'slurm'
-  clusterOptions = { "-A $params.project ${params.clusterOptions ?: ''}" }
+  clusterOptions = { clusterOptionsCreator(task.memory) }
   // Use node local storage for execution.
   scratch = '$SNIC_TMP'
 }
@@ -23,17 +57,16 @@ process {
 params {
   save_reference = true
 
-  max_memory = 125.GB
+  max_memory = 500.GB
   max_cpus = 16
   max_time = 240.h
   // illumina iGenomes reference file paths on UPPMAX
-  igenomes_base = '/sw/data/uppnex/igenomes/'
+  igenomes_base = '/sw/data/igenomes/'
 }
 
-def hostname = "hostname".execute().text.trim()
+if (hostname ==~ "s[0-9][0-9]*") {
-
+  params.max_time = 700.h
-if (hostname ==~ "b.*" || hostname ==~ "s.*") {
+  params.max_memory = 3880.GB
-  params.max_memory = 109.GB
 }
 
 if (hostname ==~ "i.*") {
@@ -42,6 +75,7 @@ if (hostname ==~ "i.*") {
 
 if (hostname ==~ "r.*") {
   params.max_cpus = 20
+  params.max_memory = 970.GB
 }
 
 profiles {

docs/maestro.md

@@ -0,0 +1,19 @@
+# nf-core/configs Maestro (at Pateur Institute, Paris) Configuration
+
+To use, run the pipeline with `-profile maestro,<qos>` (with qos being long or normal). This will download and launch the maestro.config which has been pre-configured with a setup suitable for the Maestro cluster on either the long or normal qos.
+Using one of these profiles, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline
+
+## needed Modules
+
+Please first load java, nextflow and singularity modules
+`module load java`
+`module load nextflow`
+`module load singularity`
+
+Also, do not forget to run nextflow using tmux or alike.
+
+## Other profiles at Pasteur
+
+If you are using TARS cluster, please refer to pasteur profile.
+
+Please refer to docs/pasteur.md for installing and running nf-core instructions.

docs/pipeline/eager/maestro.md

@@ -0,0 +1,30 @@
+# nf-core/configs maestro eager specific configuration
+
+Extra specific configuration for eager pipeline for human DNA data processing
+
+## Usage
+
+To use, run the pipeline with `-profile maestro,<qos>,<type>`, where qos can be normal or long and type can be nuclear or mitochondrial
+
+This will download and launch the eager specific [`maestro.config`](../../../conf/pipeline/eager/maestro.config) which has been pre-configured with a setup suitable for the Maestro cluster.
+
+Example: `nextflow run nf-core/eager -profile maestro,normal,nuclear`
+
+## eager specific configurations for maestro
+
+Specific configurations for maestro has been made for eager.
+
+We decided not to provide any tool parameters here, and focus the profile only for resource management: Maestro profiles runs with default nf-core/eager parameters, but with modifications concerning time (limit to 24h in normal qos, so increasing the memory and CPUs, specially for alignments).
+
+## nuclear
+
+Increases the number of CPUs and the amount of memory for key processes
+
+## mitochondrial
+
+More limited computational resources
+
+## unlimitedtime
+
+Every process has one year time limit. To be used only when some processes can not be completed for time reasons when using mitochondrial or nuclear profiles.  
+Expect slow processes when using this profile because only 5 CPUs are available at a time.

nfcore_custom.config

@@ -43,6 +43,7 @@ profiles {
   imperial_mb  { includeConfig "${params.custom_config_base}/conf/imperial_mb.config" }  
   jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
+  maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
   mpcdf        { includeConfig "${params.custom_config_base}/conf/mpcdf.config" }
   munin        { includeConfig "${params.custom_config_base}/conf/munin.config" }
   nu_genomics  { includeConfig "${params.custom_config_base}/conf/nu_genomics.config" }

pipeline/eager.config

@@ -11,4 +11,5 @@
 profiles {
   mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
   eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
+  maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" }
 }