Condense, improve and clean up Nextflow logging

doc/source/configuration.rst

@@ -176,7 +176,7 @@ The Nextflow configuration file is used to configure various settings for the *k
 
     * **withName** defines settings for individual processes in the *ksrates* Nextflow pipeline.
 
-      There are 11 processes in the pipeline, 6 of which (``checkConfig``, ``setupAdjustment``, ``setParalogAnalysis``, ``setOrthologAnalysis``,  ``doRateAdjustment`` and ``drawTree``) are by default run locally because they execute minimal calculations. The remaining 5 processes (``estimatePeak``, ``plotOrthologDistrib``, ``paralogsAnalyses``, ``wgdParalogs`` and ``wgdOrthologs``) are instead run by default on a cluster, if available, and can be configured under this section of the Nextflow configuration file. ``wgdParalogs`` and ``wgdOrthologs`` are the most computationally demanding and it is advised to assign them a higher computational power than the other processes. If available, we suggest to configure about 10 CPUs/cores/slots/threads and about 20GB memory (or, on average, about 2GB per configured CPU) for each of these two processes.
+      There are 11 processes in the pipeline, 6 of which (``checkConfig``, ``setupAdjustment``, ``setParalogAnalysis``, ``setOrthologAnalysis``,  ``doRateAdjustment`` and ``drawTree``) are by default run locally because they execute minimal calculations. The remaining 5 processes (``estimatePeaks``, ``plotOrthologDistrib``, ``paralogsAnalyses``, ``wgdParalogs`` and ``wgdOrthologs``) are instead run by default on a cluster, if available, and can be configured under this section of the Nextflow configuration file. ``wgdParalogs`` and ``wgdOrthologs`` are the most computationally demanding and it is advised to assign them a higher computational power than the other processes. If available, we suggest to configure about 10 CPUs/cores/slots/threads and about 20GB memory (or, on average, about 2GB per configured CPU) for each of these two processes.
 
       Settings can be tailored to your configured executor (see above) through the use of Nextflow process directives (for a complete list and detailed descriptions see the `Nextflow documentation <https://www.nextflow.io/docs/latest/process.html#process-directives>`__), such as:
 

doc/source/template_docker_nextflow.config

@@ -33,7 +33,7 @@ process {
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }
 
-    withName: 'estimatePeak' {
+    withName: 'estimatePeaks' {
         memory = ''             // e.g. '2GB'
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }

doc/source/template_nocontainer_nextflow.config

@@ -29,7 +29,7 @@ process {
         beforeScript =  ''      // e.g. 'module load python paml muscle blast'
     }
 
-    withName: 'estimatePeak' {
+    withName: 'estimatePeaks' {
         memory = ''             // e.g. '2GB'
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
         beforeScript = ''       // e.g. 'module load python'

doc/source/template_singularity_nextflow.config

@@ -35,7 +35,7 @@ process {
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }
 
-    withName: 'estimatePeak' {
+    withName: 'estimatePeaks' {
         memory = ''             // e.g. '2GB'
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }

example/nextflow.config

@@ -38,7 +38,7 @@ process {
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }
 
-    withName: 'estimatePeak' {
+    withName: 'estimatePeaks' {
         memory = ''             // e.g. '2GB'
         clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }