Update docs for hasta config

README.md

@@ -194,11 +194,13 @@ Currently documentation is available for the following pipelines within specific
   - [EVA](docs/pipeline/eager/eva.md)
 - rnafusion
   - [MUNIN](docs/pipeline/rnafusion/munin.md)
+- rnavar
+  - [MUNIN](docs/pipeline/rnavar/munin.md)
 - sarek
   - [MUNIN](docs/pipeline/sarek/munin.md)
   - [UPPMAX](docs/pipeline/sarek/uppmax.md)
-- rnavar
+- taxprofiler
-  - [MUNIN](docs/pipeline/rnavar/munin.md)
+  - [EVA](docs/pipeline/taxprofiler/eva.md)
 
 ### Pipeline-specific documentation
 

conf/eva.config

@@ -17,7 +17,7 @@ process {
     executor = 'sge'
     penv = 'smp'
     queue = 'all.q'
-    clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
+    clusterOptions = { "-S /bin/bash -V -j y -o output.sge -l h_vmem=${task.memory.toGiga()}G" }
 }
 
 executor {
@@ -37,7 +37,7 @@ profiles {
 
       process {
         queue = { task.memory > 700.GB ? 'bigmem.q' : 'archgen.q' }
-        clusterOptions = { "-S /bin/bash -V -j y -o output.log -l h_vmem=${task.memory.toGiga()}G" }
+        clusterOptions = { "-S /bin/bash -V -j y -o output.sge -l h_vmem=${task.memory.toGiga()}G" }
       }
 
       singularity {

conf/pipeline/eager/eva.config

@@ -197,6 +197,10 @@ process {
     errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
   }
   
+  withName:eigenstrat_snp_coverage {
+    beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
+  }  
+  
   withName:kraken_merge {
     beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
   }

conf/pipeline/taxprofiler/eva.config

@@ -0,0 +1,29 @@
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_description = 'nf-core/taxprofiler EVA profile provided by nf-core/configs'
+}
+
+process {
+
+    withName: BBMAP_BBDUK {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+    withName: MALT_RUN {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+    withName: METAPHLAN3 {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+    withName: MEGAN_RMA2INFO {
+    clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 4)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
+    }
+
+}

docs/pipeline/hasta.md

@@ -0,0 +1,19 @@
+# nf-core/configs: eva taxprofiler specific configuration
+
+Extra specific configuration for taxprofiler pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile hasta`.
+
+This will download and launch the taxprofiler specific [`hasta.config`](../../../conf/pipeline/taxprofiler/hasta.config) which has been pre-configured with a setup suitable for the hasta cluster.
+
+Example: `nextflow run nf-core/taxprofiler -profile hasta`
+
+## taxprofiler specific configurations for hasta
+
+Specific configurations for hasta has been made for taxprofiler.
+
+### General profiles
+
+- The general hasta profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues with: BBDUK and MALT.

docs/pipeline/taxprofiler/eva.md

@@ -0,0 +1,19 @@
+# nf-core/configs: eva taxprofiler specific configuration
+
+Extra specific configuration for taxprofiler pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile eva`.
+
+This will download and launch the taxprofiler specific [`eva.config`](../../../conf/pipeline/taxprofiler/eva.config) which has been pre-configured with a setup suitable for the MPI-EVA cluster.
+
+Example: `nextflow run nf-core/taxprofiler -profile eva`
+
+## taxprofiler specific configurations for eva
+
+Specific configurations for eva has been made for taxprofiler.
+
+### General profiles
+
+- The general MPI-EVA profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues SGE have with Java and python tools, nameling: BBDUK, MALT, MetaPhlAn3, and MEGAN

pipeline/taxprofiler.config

@@ -10,4 +10,5 @@
 
 profiles {
   hasta { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/hasta.config" }
+  eva { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/eva.config" }
 }