Add EVA and EAGER@EVA

.github/workflows/main.yml

@@ -16,7 +16,7 @@ jobs:
     needs: test_all_profiles
     strategy:
         matrix:
-          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'imperial', 'imperial_mb', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
+          profile: ['abims', 'awsbatch', 'bi','bigpurple', 'binac', 'cbe', 'ccga_dx', 'ccga_med', 'cfc', 'cfc_dev', 'crick', 'denbi_qbic', 'ebc', 'eddie', 'eva', 'genotoul', 'genouest', 'gis', 'google', 'hebbe', 'icr_davros', 'ifb_core', 'imperial', 'imperial_mb', 'jax', 'kraken', 'mpcdf', 'munin', 'oist', 'pasteur', 'phoenix', 'prince', 'seg_globe', 'shh', 'uct_hpc', 'uppmax', 'utd_ganymede', 'uzh']
     steps:
       - uses: actions/checkout@v1
       - name: Install Nextflow

conf/eva.config

@@ -49,4 +49,4 @@ profiles {
     debug {
       cleanup = false
     }
-}
+}

conf/pipeline/eager/eva.config

@@ -9,10 +9,12 @@ params {
 // Specific nf-core/eager process configuration
 process {
 
+  beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -XX:+PrintCommandLineFlags"'
+
   maxRetries = 2
 
   // Solution for clusterOptions comes from here: https://github.com/nextflow-io/nextflow/issues/332 + personal toMega conversion
-  clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toMega().toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().toString().replaceAll(/[\sB]/,'')}M" }
+  clusterOptions = { "-S /bin/bash -j y -o output.log -l h_vmem=${task.memory.toGiga()}G,virtual_free=${task.memory.toGiga()}G" }
 
   withLabel:'sc_tiny'{
     cpus = { check_max( 1, 'cpus' ) }
@@ -59,63 +61,64 @@ process {
   // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
 
   withName: makeSeqDict {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -v JAVA_OPTS='-XX:ParallelGCThreads=1' -l h_vmem=${(task.memory.toGiga() + 3)}G,virtual_free=${(task.memory.toGiga() + 3)}G" }
    }
       
   withName: fastqc {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: adapter_removal {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(12000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(12000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: dedup {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: markduplicates {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(8000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(8000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
    }
 
   withName: malt {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: maltextract {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: multivcfanalyzer {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: mtnucratio {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: vcf2genome {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: qualimap {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
    }
 
   withName: damageprofiler {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(5000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() + 6)}G,virtual_free=${(task.memory.toGiga() + 6)}G" }
    }
 
   withName: circularmapper {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: circulargenerator {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(1000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
    }
 
   withName: preseq {
-    clusterOptions = { "-S /bin/bash -l h_vmem=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M,virtual_free=${task.memory.toMega().plus(4000).toString().replaceAll(/[\sB]/,'')}M" }
+    clusterOptions = { "-S /bin/bash -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'ignore' }
    }
 
 }
@@ -209,4 +212,4 @@ profiles {
       bwaalnl = 16500
      }
   }
-}
+}

docs/eva.md

@@ -25,4 +25,4 @@ Note the following characteristics of this profile:
 
 ### debug
 
-This simple profile just turns off automatic clean up of intermediate files. This can be useful for debugging. Specify e.g. with `-profile eva,archgen`
+This simple profile just turns off automatic clean up of intermediate files. This can be useful for debugging. Specify e.g. with `-profile eva,archgen`

docs/pipeline/eager/eva.md

@@ -31,4 +31,4 @@ Specific configurations for eva has been made for eager.
 #### Pathogen
 
 - `pathogen_loose`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 16 -n 0.01`)
-- `pathogen_strict`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 32, -n 0.1`)
+- `pathogen_strict`: optimised for mapping of human aDNA reads (i.e. bwa aln defaults as `-l 32, -n 0.1`)