Merge pull request #154 from jfy133/master

Update SHH nf-core/eager group-specific profiles

conf/pipeline/eager/shh.config

@@ -5,6 +5,10 @@ params {
   config_profile_contact = 'James Fellows Yates (@jfy133)'
   config_profile_description = 'nf-core/eager SHH profile provided by nf-core/configs'
   igenomes_base = "/projects1/public_data/igenomes/"
+  
+  // default BWA
+   bwaalnn = 0.04
+   bwaalnl = 32
 }
 
 // Specific nf-core/eager process configuration
@@ -18,7 +22,26 @@ process {
   }
 }
 
-params {
+profiles {
-    bwaalnn = 0.01
+  pathogen_loose {
-    bwaalnl = 32
+    params {
+      config_profile_description = 'Pathogen (loose) MPI-SHH profile, provided by nf-core/configs.'
+      bwaalnn = 0.01
+      bwaalnl = 16
+    }
+  }
+  pathogen_strict {
+    params {
+      config_profile_description = 'Pathogen (strict) MPI-SHH SDAG profile, provided by nf-core/configs.'
+      bwaalnn = 0.1
+      bwaalnl = 32
+     }
+  }
+  human {
+      params {
+      config_profile_description = 'Human MPI-SHH SDAG profile, provided by nf-core/configs.'
+      bwaalnn = 0.01
+      bwaalnl = 16500
+     }
+  }
 }

conf/shh.config

@@ -3,6 +3,11 @@ params {
   config_profile_description = 'Generic MPI-SHH cluster(s) profile provided by nf-core/configs.'
   config_profile_contact = 'James Fellows Yates (@jfy133), Maxime Borry (@Maxibor)'
   config_profile_url = 'https://shh.mpg.de'
+  max_memory = 256.GB
+  max_cpus = 32
+  max_time = 720.h
+  //Illumina iGenomes reference file path
+  igenomes_base = "/projects1/public_data/igenomes/"
 }
 
 cleanup = true
@@ -23,21 +28,17 @@ executor {
     queueSize = 16
 }
 
-params {
-  max_memory = 256.GB
-  max_cpus = 32
-  max_time = 720.h
-  //Illumina iGenomes reference file path
-  igenomes_base = "/projects1/public_data/igenomes/"
-}
-
 profiles {
   cdag {
-      config_profile_description = 'MPI-SHH CDAG profile, provided by nf-core/configs.'
+    params {
+      config_profile_description = 'CDAG MPI-SHH profile, provided by nf-core/configs.'
+    }
   }
   sdag {
-      config_profile_description = 'MPI-SHH SDAG profile, provided by nf-core/configs.'
+    params {
+      config_profile_description = 'SDAG MPI-SHH profile, provided by nf-core/configs.'
       max_memory = 2.TB
       max_cpus = 128
+     }
   }
 }

docs/pipeline/eager/shh.md

@@ -14,5 +14,5 @@ Example: `nextflow run nf-core/eager -profile shh`
 
 Specific configurations for shh has been made for eager.
 
-* If running with the MALT module turned on, the MALT process by default will be sent  to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail.
+* If running with the MALT module turned on, the MALT process by default will be sent  to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. Note, this will only work on SDAG.
-* Modifies the bwa aln `-n` parameter to 0.01, rather than typical default of 0.04, and `-l` to 32 (rather than 1024) to syncronise the (unpublished) parameter with EAGER1 and typical/expected usage within the department.
+* Provides additional group specific profiles, which adapt the `bwa aln` mapping parameters to each context: `pathogens_loose` (`-l 0.01 -n 16`), `pathogens_strict` (`-l 32, -n 0.1`) and `human` (`-l 16500, -n 0.01`).