Condense, improve and clean up Nextflow logging (#25)

* Condense, improve and clean up Nextflow logging
- tries to remedy visual issues in ANSI console by condensing and
  shortening line lengths of log output
- improves some wording, consistency and whitespacing of log output
- refactor some log output code into functions
- adds ksrates version to log

* Don't clean up if ksrates config file newly generated
There won't be anything to clean up, and onComplete would print
irrelevant warning about empty focal_species parameter.

* Single '/' in logs folder path when focal_species empty

* Some renaming of channels and variables
- Correction -> Adjustment
- peakCalling -> paralogsAnalyses

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'
     }