diff --git a/doc/source/_images/error_box2.png b/doc/source/_images/error_box2.png
index 5fcb61d..1648cc6 100644
Binary files a/doc/source/_images/error_box2.png and b/doc/source/_images/error_box2.png differ
diff --git a/doc/source/configuration.rst b/doc/source/configuration.rst
index d0e25e9..cb3eadb 100644
--- a/doc/source/configuration.rst
+++ b/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:
     
diff --git a/doc/source/template_docker_nextflow.config b/doc/source/template_docker_nextflow.config
index f9a0bed..1105593 100644
--- a/doc/source/template_docker_nextflow.config
+++ b/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'
     }
diff --git a/doc/source/template_nocontainer_nextflow.config b/doc/source/template_nocontainer_nextflow.config
index 28046ff..e88d111 100644
--- a/doc/source/template_nocontainer_nextflow.config
+++ b/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'
diff --git a/doc/source/template_singularity_nextflow.config b/doc/source/template_singularity_nextflow.config
index 8a52b18..5e6fb6b 100644
--- a/doc/source/template_singularity_nextflow.config
+++ b/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'
     }
diff --git a/example/nextflow.config b/example/nextflow.config
index 3c82876..a78e87c 100644
--- a/example/nextflow.config
+++ b/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'
     }
diff --git a/main.nf b/main.nf
index e9b97b1..ca2155c 100755
--- a/main.nf
+++ b/main.nf
@@ -1,6 +1,8 @@
 #!/usr/bin/env nextflow
 
-LOG = true  // should probably use our own Logger...
+// should probably use our own Logger...
+LOG_OUTPUT = true  // log process and other output via log.info
+LOG_PROCESS_INFO = false  // log process details before submission
 
 /*
  * Pipeline input parameters
@@ -11,28 +13,40 @@ params.preserve = false
 
 // giving the configuration file through the "input" process section
 configfile = file(params.config)
+if (configfile.isEmpty()) {
+     newConfigFile = true
+} else {
+     newConfigFile = false
+}
 
+log.info ""
 log.info ""
 log.info """\
-         K S R A T E S   -   N E X T F L O W   P I P E L I N E
-         -----------------------------------------------------
+         K S R A T E S   -   N E X T F L O W   P I P E L I N E   (v1.0)
+         --------------------------------------------------------------
          
          Configuration file:                    $params.config
          Logs folder:                           logs_${workflow.sessionId.toString().substring(0,8)}
          Preserve leftover files:               $params.preserve
          """
          .stripIndent()
-log.info ""
 
-log.info "Cmd line:       $workflow.commandLine"
-log.info "Launch dir:     $workflow.launchDir"
-log.info "Work dir:       $workflow.workDir"
-log.info "Project:        $workflow.projectDir"
-//log.info "PWD:            $PWD"
-//log.info "Base dir:       $baseDir"
-//log.info "Logs folder:    logs_${workflow.sessionId.toString().substring(0,8)}"
-// log.info "Session ID:     $workflow.sessionId"
-// log.info "Stats:          $workflow.stats"
+log.info "Command line:               $workflow.commandLine"
+log.info "Launch directory:           $workflow.launchDir"
+//log.info "PWD:                        $PWD"
+log.info "Work directory:             $workflow.workDir"
+//log.info "Base dir:                   $baseDir"
+log.info "ksrates directory:          $workflow.projectDir"
+//log.info "ksrates Git repo:           $workflow.repository"
+//log.info "ksrates Git revision:       $workflow.revision"
+//log.info "ksrates container:          $workflow.container"
+//log.info "ksrates container engine:   $workflow.containerEngine"
+//log.info "Configuration files:        $workflow.configFiles"
+//log.info "Session ID:                 $workflow.sessionId"
+//log.info "Stats:                      $workflow.stats"
+log.info ""
+log.info "Start time:                 $workflow.start"
+log.info ""
 log.info ""
 
 /*
@@ -42,16 +56,35 @@ log.info ""
 try {
     NXF_ANSI_LOG
 } catch (Exception e) {
-    NXF_ANSI_LOG = true
+    NXF_ANSI_LOG = "true"
 }
 
+//log.info "NXF_ANSI_LOG: $NXF_ANSI_LOG"
+
+// command-line option -ansi-log has preference over NXF_ANSI_LOG
+if ( workflow.commandLine.containsIgnoreCase("-ansi-log true") ) {
+    ansiLog = true
+} else if ( workflow.commandLine.containsIgnoreCase("-ansi-log false") ) {
+    ansiLog = false
+} else if ( workflow.commandLine.containsIgnoreCase("-bg") ) {
+    // Nextflow -bg option turns ANSI log off (unless explicit -ansi-log true)
+    ansiLog = false
+} else if ( NXF_ANSI_LOG.equalsIgnoreCase("false") ) {
+    ansiLog = false
+} else {
+    // default should be true
+    ansiLog = true
+}
+//log.info "ansiLog: $ansiLog"
+
+
 // Dictionary mapping each process with the associated log file
 logs_names = [
 "checkConfig" : null,
 "setupAdjustment" : "setup_adjustment.log",
 "setParalogAnalysis" : "wgd_paralogs.log",
 "setOrthologAnalysis": "set_orthologs.log",
-"estimatePeak": "estimate_peak.log", 
+"estimatePeaks": "estimate_peaks.log",
 "wgdParalogs": "wgd_paralogs.log", 
 "wgdOrthologs": "wgd_orthologs_",
 "plotOrthologDistrib": "plot_ortholog_distributions.log", 
@@ -60,6 +93,52 @@ logs_names = [
 "drawTree": "rate_adjustment.log" ]
 
 
+/*
+ * Function to log various process information before submission/execution
+ * if print is set to true or if any process setting deviates from defaults
+ * (executor = 'local', cpus = 1, and no memory setting).
+ */
+def logProcessInfo(task, speciesLabel="", printIndex=false, print=LOG_PROCESS_INFO) {
+    if (print || task.executor != 'local' || task.cpus != 1 || task.memory) {
+        log.info "[${task.process}]${ speciesLabel ? ' [' + speciesLabel + '] ' : ' ' }" +\
+                 "Process${ printIndex ? ' (' + task.index + ') ' : ' ' }" +\
+                 "queued on executor '${task.executor}' with " +\
+                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' }" +\
+                 "${ task.memory ? ' and ' + task.memory : '' }"
+    }
+}
+
+/*
+ * Function to log process output to stdout/console (if print is set to true).
+ * Each non-empty log line will have the given processName prepended in square brackets.
+ * Note that the output will be logged all together only after the process terminates.
+ */
+def logProcessOutput(out, processName, print=LOG_OUTPUT) {
+    if (print) {
+        out.splitText() {
+            if ( it.equals("\n") ) {
+                // remove newline since subsequent log.info will append another one
+                ""
+            } else if ( it.endsWith("\n") ) {
+                // remove newline since subsequent log.info will append another one
+                "[$processName] " + it.replace('\n', '')
+            } else {
+                "[$processName] $it"
+            }
+        }
+        .subscribe {
+            if ( "".equals(it) && ansiLog ) {
+                // ignore, i.e. do not print empty lines if ansiLog is true
+                // to make output more compact
+            } else {
+                log.info it.trim()
+            }
+        }
+    }
+}
+
+
+
 process checkConfig {
 
     executor 'local'
@@ -69,20 +148,28 @@ process checkConfig {
         file config from configfile
     
     output:
-        stdout outcheckConfig
-        env trigger_pipeline into trigger_setupCorrection_channel
+        stdout outCheckConfig
+        env trigger_pipeline into trigger_setupAdjustment_channel
 
     script:
+    logProcessInfo(task)
     """
     processDir=\$PWD
     cd $PWD
 
     if [ ! -f ${config} ]; then
-        echo "Configuration file [${config}] not found: it will be now generated"
-        echo "Please fill in with the required parameters:"
-        echo "species, newick_tree, latin_names, fasta_filenames and if applicable gff_filename, gff_feature and gff_attribute"
-        echo "Then rerun the Nextflow pipeline."
+        echo ""
+        echo -n "Configuration file [${config}] not found: it will now be generated... "
+
         ksrates generate-config ${config} >> \$processDir/generate_config.txt
+        RET_CODE=\$?
+        echo "done [\${RET_CODE}]"
+
+        echo "Please fill in the required parameters:"
+        echo " focal_species, newick_tree, latin_names, fasta_filenames, and"
+        echo " gff_filename, gff_feature and gff_attribute (if applicable)"
+        echo "Then rerun the Nextflow pipeline"
+
         trigger_pipeline=false
     else
         trigger_pipeline=true
@@ -91,21 +178,8 @@ process checkConfig {
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process checkConfig terminates)
- */
-if (LOG) {
-    outcheckConfig
-        .splitText() {
-            if ( it.endsWith("\n") ) {
-                "[checkConfig] " + it.replace('\n', '')
-            } else {
-                "[checkConfig] $it"
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console (always, i.e. no matter if LOG_OUTPUT).
+logProcessOutput(outCheckConfig, "checkConfig", true)
 
 
 
@@ -120,30 +194,29 @@ process setupAdjustment {
 
     input:
         file config from configfile
-        val trigger_pipeline from trigger_setupCorrection_channel
+        val trigger_pipeline from trigger_setupAdjustment_channel
 
     output:
-        stdout outsetupAdjustment
+        stdout outSetupAdjustment
         env species into species_channel
         env logs_folder into logs_folder_channel
         file "ortholog_pairs_*.tsv" into check_ortholog_pairs_channel
-        env trigger_plot_orthologs into trigger_plotOrtholog_from_setupCorrection_channel
+        env trigger_plot_orthologs into trigger_plotOrtholog_from_setupAdjustment_channel
 
     when:
         trigger_pipeline == "true"
 
     script:
-    if (LOG) {
-        log.info "Process setupAdjustment (${task.index}) has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task)
     """
+    echo ""
     trigger_plot_orthologs=false
 
     processDir=\$PWD
     cd $PWD
 
     species=`grep "^[[:space:]]*focal_species[[:space:]]*=" ${config} | cut -d "=" -f 2 | xargs`
+    echo "Focal species: \$species"
 
     # Generating folders for output files, especially to have the log_folder since the very beginning
     if [ ! -d rate_adjustment ]; then
@@ -159,48 +232,41 @@ process setupAdjustment {
     logs_folder="rate_adjustment/\$species/logs_\$workID"
 
 
-    echo "[\$species] Extracting ortholog pairs from Newick tree"
+    echo -n "Extracting ortholog species pairs and trios from Newick tree... "
     echo "NF internal work directory for [setupAdjustment] process:\n\$processDir\n" > \${logs_folder}/${logs_names["setupAdjustment"]}
 
     ksrates init ${config} --nextflow >> \${logs_folder}/${logs_names["setupAdjustment"]} 2>&1
+    RET_CODE=\$?
+    echo "done [\${RET_CODE}]"
+
     cat rate_adjustment/\$species/ortholog_pairs_\${species}.tsv > \${processDir}/ortholog_pairs_\${species}.tsv
 
     # If all the ortholog data are present in the databases, already trigger plotOrthologs to plot the ortholog distributions
     if [ -z "`tail -n +2 rate_adjustment/\$species/ortholog_pairs_\${species}.tsv`" ]; then    # if file size NOT greater than 0, so if the file is empty and there aren't unknown pairs
+        echo "All ortholog species pair data already present in ortholog databases"
         trigger_plot_orthologs=true
     else
-        echo "Ortholog data in DB and / or TSV files not present for one or more species pair required for rate-adjustment"
-        echo "Ortholog Ks analysis is scheduled"
-        echo "The species pair list can be found in [rate_adjustment/\$species/ortholog_pairs_\${species}.tsv]"
+        echo "The list of required ortholog species pairs can be found in:"
+        echo " rate_adjustment/\$species/ortholog_pairs_\${species}.tsv"
+        echo "The list of ortholog species trios can be found in:"
+        echo " rate_adjustment/\$species/ortholog_trios_\${species}.tsv"
     fi
 
-    echo "[\$species] log can be found in: \${logs_folder}/${logs_names["setupAdjustment"]}"
-    
+    echo "Log can be found in:"
+    echo " \${logs_folder}/${logs_names["setupAdjustment"]}"
+
     cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process setupAdjustment terminates)
- */
-if (LOG) {
-    outsetupAdjustment
-        .splitText() {
-            if ( it.endsWith("\n") ) {
-                "[setupAdjustment] " + it.replace('\n', '')
-            } else {
-                "[setupAdjustment] $it"
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outSetupAdjustment, "setupAdjustment")
 
 
 
 /*
- * Process that checks if the .ks.tsv file containing the paralog Ks values
- * for the focal species is already present. If not, triggers 
+ * Process that checks if the .ks.tsv file(s) containing the paralog Ks values
+ * for the focal species are already present. If not, triggers
  * wgdParalogs for their estimate.
  */ 
 process setParalogAnalysis {
@@ -214,19 +280,17 @@ process setParalogAnalysis {
         file config from configfile
 
     output:
-        stdout outsetParalogAnalysis
+        stdout outSetParalogAnalysis
         env trigger_wgdPara into trigger_wgdPara_channel
-        env trigger_doRateCorrection_from_para into trigger_doRateCorrection_from_setParalog_channel
+        env trigger_doRateAdjustment_from_para into trigger_doRateAdjustment_from_setParalog_channel
 
     script:
-    if (LOG) {
-        log.info "Process setParalogAnalysis (${task.index}) has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task)
     """
-    echo "[$species] Organizing paralog wgd runs"
+    echo ""
+    echo "[$species] Setting up paralog wgd analysis for focal species"
 
-    trigger_doRateCorrection_from_para=false
+    trigger_doRateAdjustment_from_para=false
     trigger_wgdPara=false
 
     paranome_status="not_required"
@@ -238,13 +302,13 @@ process setParalogAnalysis {
     processDir=\$PWD
     cd $PWD
 
-    echo "NF internal work directory for [setParalogAnalysis (${task.index})] process:\n\$processDir\n" > $logs_folder/${logs_names["setParalogAnalysis"]}
+    echo "NF internal work directory for [setParalogAnalysis] process:\n\$processDir\n" > $logs_folder/${logs_names["setParalogAnalysis"]}
 
     # Triggering wgdParalog process only if ".ks.tsv" (and ".ks_anchors.tsv") files are missing
 
     if [ \${paranome} = "yes" ]; then
         if [ ! -f paralog_distributions/wgd_${species}/${species}.ks.tsv ]; then
-            echo "[$species] Paralog TSV file not found [${species}.ks.tsv]; wgd pipeline will be started"
+            echo "[$species] Will run whole-paranome wgd analysis"
             echo "[$species] Paralog TSV file not found [${species}.ks.tsv]" >> $logs_folder/${logs_names["setParalogAnalysis"]}
             echo "[$species] Whole-paranome wgd pipeline will be started\n" >> $logs_folder/${logs_names["setParalogAnalysis"]}
             paranome_status="todo"
@@ -254,9 +318,9 @@ process setParalogAnalysis {
     fi
     if [ \${colinearity} = "yes" ]; then
         if [ ! -f paralog_distributions/wgd_${species}/${species}.ks_anchors.tsv ]; then
-            echo "[$species] Anchor pairs TSV file not found [${species}.ks_anchors.tsv]; wgd pipeline will be started"
+            echo "[$species] Will run anchor-pair (collinearity) wgd analysis"
             echo "[$species] Anchor pairs TSV file not found [${species}.ks_anchors.tsv]" >> $logs_folder/${logs_names["setParalogAnalysis"]}
-            echo "[$species] Co-linearity wgd pipeline will be started\n" >> $logs_folder/${logs_names["setParalogAnalysis"]}
+            echo "[$species] Collinearity wgd pipeline will be started\n" >> $logs_folder/${logs_names["setParalogAnalysis"]}
             colinearity_status="todo"
         else
             colinearity_status="already_done"
@@ -267,39 +331,29 @@ process setParalogAnalysis {
         # Trigger wgdParalog process to get the missing tsv file(s)
         trigger_wgdPara=true
     else
-        echo "[$species] Paralog TSV file(s) already present; skipping paralog wgd pipeline"
+        echo "[$species] Paralog data already present; skipping paralog wgd analysis"
         echo "[$species] Paralog TSV file(s) already present; skipping paralog wgd pipeline\n" >> $logs_folder/${logs_names["setParalogAnalysis"]}
         
         # Trigger doRateAdjustment process to plot (at least) the paralog distribution in the mixed plot
-        trigger_doRateCorrection_from_para=true
+        trigger_doRateAdjustment_from_para=true
     fi
 
     echo "----------------------------------------------------------------\n" >> $logs_folder/${logs_names["setParalogAnalysis"]}
-    echo "[$species] log can be found in: $logs_folder/${logs_names["setParalogAnalysis"]}"
+    echo "[$species] Log can be found in:"
+    echo "[$species]  $logs_folder/${logs_names["setParalogAnalysis"]}"
+
     cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process setParalogAnalysis terminates)
- */
-if (LOG) {
-    outsetParalogAnalysis
-        .splitText() {
-            if ( it.endsWith("\n") ) {
-                "[setParalogAnalysis] " + it.replace('\n', '')
-            } else {
-                "[setParalogAnalysis] $it"
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outSetParalogAnalysis, "setParalogAnalysis")
+
 
 
 /*
  * Process that receives the list of all species pairs missing in database and that 
- * 1) triggers wgdOrthologs for pairs without the ks.tsv file and/or 2) triggers EstimatePeak
+ * 1) triggers wgdOrthologs for pairs without the ks.tsv file and/or 2) triggers estimatePeaks
  * for pairs without ortholog peak data in database but that do have the .ks.tsv file.
  */
 process setOrthologAnalysis {
@@ -313,51 +367,54 @@ process setOrthologAnalysis {
         file config from configfile
 
     output:
-        stdout outsetOrthologAnalysis
+        stdout outSetOrthologAnalysis
         file "tmp_species_pairs_for_wgdOrtholog.txt" optional true into species_pairs_for_wgd_Orthologs_channel
         file "tmp_species_pairs_for_estimatePeak.txt" optional true into file_for_estimatePeak_channel
         env estimatePeak_not_needed into trigger_plotOrthologs_together_with_wgdOrtholog_channel
         env wgdOrtholog_not_needed into trigger_plotOrthologs_together_with_estimatePeak_channel
 
     script:
-    if (LOG) {
-        log.info "Process setOrthologAnalysis (${task.index}) has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task)
     """
+    echo ""
+    echo "Setting up required ortholog analyses"
+
     processDir=\$PWD
     cd $PWD
 
-    echo "NF internal work directory for [setOrthologAnalysis (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["setOrthologAnalysis"]}
+    echo "NF internal work directory for [setOrthologAnalysis] process:\n\$processDir\n" >> $logs_folder/${logs_names["setOrthologAnalysis"]}
 
     wgdOrtholog_not_needed=false
     estimatePeak_not_needed=false
 
-    # If the file for the species pair is empty, then setOrthologAnalysis skips the ortholog Ks estimate and peak estimate steps. 
+    # If the file with the ortholog species pairs is empty, then Ks estimation and peak estimation steps are skipped.
     if [ -z "`tail -n +2 \${processDir}/$ortholog_pairs`" ]; then
-        echo "No species pairs are listed for wgd ortholog pipeline or ortholog peak estimate."
+        echo "No ortholog species pairs listed; skipping ortholog wgd and peak analyses"
         echo "No species pairs are listed for wgd ortholog pipeline or ortholog peak estimate." >> $logs_folder/${logs_names["setOrthologAnalysis"]}
     fi 
 
     while read -r species1 species2 || [ -n "\$species1" ]; do
         if [ ! -f ortholog_distributions/wgd_\${species1}_\${species2}/\${species1}_\${species2}.ks.tsv ]; then
             echo "\$species1\t\$species2" >> \${processDir}/tmp_species_pairs_for_wgdOrtholog.txt
+            echo "[\$species1 – \$species2] Will run ortholog wgd analysis"
             echo "[\$species1 – \$species2] Ortholog TSV file not present [\${species1}_\${species2}.ks.tsv]" >> $logs_folder/${logs_names["setOrthologAnalysis"]}
             echo "[\$species1 – \$species2] Ortholog wgd pipeline will be started" >> $logs_folder/${logs_names["setOrthologAnalysis"]}
         else
+            echo "[\$species1 – \$species2] Will run ortholog peak analysis"
             echo "[\$species1 – \$species2] Ortholog TSV file already present; skipping ortholog wgd pipeline" >> $logs_folder/${logs_names["setOrthologAnalysis"]}
             echo "[\$species1 – \$species2] Update of ortholog database(s) will be started." >> $logs_folder/${logs_names["setOrthologAnalysis"]}
 
-            if [ ! -f \${processDir}/tmp_species_pairs_for_estimatePeak.txt ]; then   # if the file does not exist yet, add headers
+            # if the tmp file does not exist yet, add headers
+            if [ ! -f \${processDir}/tmp_species_pairs_for_estimatePeak.txt ]; then
                 echo "Species1\tSpecies2" >> \${processDir}/tmp_species_pairs_for_estimatePeak.txt
             fi
             echo "\$species1\t\$species2" >> \${processDir}/tmp_species_pairs_for_estimatePeak.txt   # add a species pair
         fi
         echo " \n----------------------------------------------------------------\n" >> $logs_folder/${logs_names["setOrthologAnalysis"]}
-        echo "[\$species1 – \$species2] log can be found in: $logs_folder/${logs_names["setOrthologAnalysis"]}"
     done < <(tail -n +2 \${processDir}/$ortholog_pairs) # skipping the headers
 
-    if [ ! -s \${processDir}/tmp_species_pairs_for_wgdOrtholog.txt ]; then    # if the file for wgdOrthologs is empty (size not > 0)
+    # if the file for wgdOrthologs is empty (size not > 0)
+    if [ ! -s \${processDir}/tmp_species_pairs_for_wgdOrtholog.txt ]; then
         wgdOrtholog_not_needed=true
     else
         if [ ! -d ortholog_distributions ]; then
@@ -365,38 +422,29 @@ process setOrthologAnalysis {
         fi
     fi
 
-    if [ -z "`tail -n +2 \${processDir}/tmp_species_pairs_for_estimatePeak.txt`" ]; then    # if the file content for estimatePeaks (skipping headers) is empty (empty string check)
+    # if the file content for estimatePeaks (skipping headers) is empty (empty string check)
+    if [ -z "`tail -n +2 \${processDir}/tmp_species_pairs_for_estimatePeak.txt`" ]; then
         estimatePeak_not_needed=true
     fi
 
+    echo "Log can be found in:"
+    echo " $logs_folder/${logs_names["setOrthologAnalysis"]}"
+
     cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process setOrthologAnalysis terminates)
- */
-if (LOG) {
-    outsetOrthologAnalysis
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[setOrthologAnalysis] " + it.replace('\n', '') 
-            } else {
-                "[setOrthologAnalysis] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outSetOrthologAnalysis, "setOrthologAnalysis")
 
 
 
 /*
- * Process that estimates the ortholog Ks distribution peak for a species pair 
- * that has already its .ks.tsv file, but that for some reasons 
- * is not present anymore in the ortholog database(s) (i.e. has been deleted).
+ * Process that estimates the ortholog Ks distribution peak for species pairs
+ * that have already their .ks.tsv files, but that for some reasons
+ * are not present anymore in the ortholog database(s) (i.e. have been deleted).
  */
-process estimatePeak {
+process estimatePeaks {
 
     input:
         file species_pairs_for_peak from file_for_estimatePeak_channel
@@ -404,42 +452,36 @@ process estimatePeak {
         file config from configfile
         
     output:
-        stdout outestimatePeak
-        val true into trigger_doRateCorrection_from_estimatePeak_channel
+        stdout outEstimatePeaks
+        val true into trigger_doRateAdjustment_from_estimatePeak_channel
         val true into trigger_plotOrtholog_from_estimatePeak_channel
         val true into trigger_plotOrtholog_from_estimatePeak_together_with_wgdOrthologs_channel
 
     script:
-    if (LOG) {
-        log.info "Process estimatePeak (${task.index}) has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task)
     """
+    echo ""
+    echo -n "`date "+%T"` Starting missing ortholog peak analyses... "
+
     processDir=\$PWD
     cd $PWD
+    echo "NF internal work directory for [estimatePeaks (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["estimatePeaks"]}
 
-    echo "NF internal work directory for [estimatePeak (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["estimatePeak"]}
-    echo "Updating ortholog peak database" >> $logs_folder/${logs_names["estimatePeak"]}
+    echo "Updating ortholog peak database" >> $logs_folder/${logs_names["estimatePeaks"]}
 
-    ksrates orthologs-analysis ${config} --ortholog-pairs=\$processDir/$species_pairs_for_peak >> $logs_folder/${logs_names["estimatePeak"]} 2>&1
+    ksrates orthologs-analysis ${config} --ortholog-pairs=\$processDir/$species_pairs_for_peak >> $logs_folder/${logs_names["estimatePeaks"]} 2>&1
+    RET_CODE=\$?
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
+    echo "Log can be found in:"
+    echo " $logs_folder/${logs_names["estimatePeaks"]}"
+
+    cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process estimatePeak terminates)
- */
-if (LOG) {
-    outestimatePeak
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[estimatePeak] " + it.replace('\n', '') 
-            } else {
-                "[estimatePeak] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outEstimatePeaks, "estimatePeaks")
 
 
 
@@ -457,53 +499,37 @@ process wgdParalogs {
 
     output:
         stdout outParalogs
-        val true into trigger_doRateCorrection_from_wgdParalog_channel
+        val true into trigger_doRateAdjustment_from_wgdParalog_channel
 
     when:
         trigger_wgdPara == "true"
 
     script:
-    if (LOG) {
-        log.info "Process wgdParalogs (${task.index}) will use species $species and has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task, species, printIndex=false, print=true)
     """
-    echo "[$species] `date`"
-    echo "[$species] Starting paralog wgd analysis"
+    echo ""
+    echo -n "[$species] `date "+%T"` Starting paralog wgd analysis... "
 
     processDir=\$PWD
     cd $PWD
-    echo "NF internal work directory for [wgdParalogs] process:\n\$processDir\n" >> $logs_folder/${logs_names["wgdParalogs"]}
+    echo "NF internal work directory for [wgdParalogs (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["wgdParalogs"]}
 
     echo "Using ${task.cpus} thread(s)\n">> $logs_folder/${logs_names["wgdParalogs"]}
     echo "[$species] Using ${task.cpus} thread(s)"
 
     ksrates paralogs-ks ${config} --n-threads=${task.cpus} >> $logs_folder/${logs_names["wgdParalogs"]} 2>&1
-
     RET_CODE=\$?
-    echo "[$species] Done [\${RET_CODE}]"
-    echo "[$species] wgd log can be found in: $logs_folder/${logs_names["wgdParalogs"]}"
-    echo "[$species] `date`"
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
+    echo "[$species] wgd log can be found in:"
+    echo "[$species]  $logs_folder/${logs_names["wgdParalogs"]}"
 
     cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process wgdParalogs terminates)
- */
-if (LOG) {
-    outParalogs
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[wgdParalogs] " + it.replace('\n', '') 
-            } else {
-                "[wgdParalogs] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outParalogs, "wgdParalogs")
 
 
 
@@ -521,58 +547,43 @@ process wgdOrthologs {
 
     output:
         stdout outOrthologs
-        val true into trigger_doRateCorrection_from_wgdOrtholog_channel
+        val true into trigger_doRateAdjustment_from_wgdOrtholog_channel
         val true into trigger_plotOrtholog_from_wgdOrtholog_channel
         val true into trigger_plotOrtholog_from_wgdOrtholog_together_with_estimatePeak_channel
 
     script:
-    if (LOG) {
-        log.info "Process wgdOrthologs (${task.index}) will use species pair $species1 – $species2 and has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task, "$species1 – $species2", printIndex=true, print=true)
     """
-    echo "[$species1 – $species2] `date`"
-    echo "[$species1 – $species2] Starting ortholog wgd analysis"
+    echo ""
+    echo -n "[$species1 – $species2] `date "+%T"` Starting ortholog wgd analysis... "
 
     processDir=\${PWD}
     cd $PWD
     echo "NF internal work directory for [wgdOrthologs (${task.index})] process:\n\$processDir\n" > $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log
 
     echo "Using ${task.cpus} thread(s)\n">> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log
-    echo "[$species1 – $species2] Using ${task.cpus} thread(s)"
+#    echo "[$species1 – $species2] Using ${task.cpus} thread(s)"
 
     ksrates orthologs-ks ${config} $species1 $species2 --n-threads=${task.cpus} >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log 2>&1
     RET_CODE=\$?
-    echo "[$species1 – $species2] wgd done [\${RET_CODE}]"
+    echo "done [\${RET_CODE}] `date "+%T"`"
     
-    echo "[$species1 – $species2] Computing ortholog peak and error"
+    echo -n "[$species1 – $species2] `date "+%T"` Starting ortholog peak analysis... "
+    echo "\n" >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log
     echo "Species1\tSpecies2\n$species1\t$species2" > \${processDir}/tmp_${species1}_${species2}.txt
     ksrates orthologs-analysis ${config} --ortholog-pairs=\${processDir}/tmp_${species1}_${species2}.txt >> $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log 2>&1
-
     RET_CODE=\$?
-    echo "[$species1 – $species2] Compute peak done [\${RET_CODE}]"
-    echo "[$species1 – $species2] wgd log and compute peak log can be found in: $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log"
-    echo "[$species1 – $species2] `date`"
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
+    echo "[$species1 – $species2] wgd log and peak analysis log can be found in:"
+    echo "[$species1 – $species2]  $logs_folder/${logs_names["wgdOrthologs"]}${species1}_${species2}.log"
 
     cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process wgdOrthologs terminates)
- */
-if (LOG) {
-    outOrthologs
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[wgdOrthologs] " + it.replace('\n', '') 
-            } else {
-                "[wgdOrthologs] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outOrthologs, "wgdOrthologs")
 
 
 
@@ -586,12 +597,12 @@ process plotOrthologDistrib {
 
     input:
         val species from species_channel
-        val trigger from trigger_plotOrtholog_from_setupCorrection_channel.mix(trigger_plotOrtholog_from_estimatePeak_together_with_wgdOrthologs_channel.merge(trigger_plotOrtholog_from_wgdOrtholog_together_with_estimatePeak_channel.collect()), trigger_plotOrthologs_together_with_wgdOrtholog_channel.merge(trigger_plotOrtholog_from_wgdOrtholog_channel.collect()), trigger_plotOrthologs_together_with_estimatePeak_channel.merge(trigger_plotOrtholog_from_estimatePeak_channel))
+        val trigger from trigger_plotOrtholog_from_setupAdjustment_channel.mix(trigger_plotOrtholog_from_estimatePeak_together_with_wgdOrthologs_channel.merge(trigger_plotOrtholog_from_wgdOrtholog_together_with_estimatePeak_channel.collect()), trigger_plotOrthologs_together_with_wgdOrtholog_channel.merge(trigger_plotOrtholog_from_wgdOrtholog_channel.collect()), trigger_plotOrthologs_together_with_estimatePeak_channel.merge(trigger_plotOrtholog_from_estimatePeak_channel))
         val logs_folder from logs_folder_channel
         file config from configfile
 
     output:
-        stdout outplotOrthologDistrib
+        stdout outPlotOrthologDistrib
 
     when:
         trigger == "true" || !trigger.contains("false")
@@ -604,48 +615,34 @@ process plotOrthologDistrib {
          * ["false"/"true", many true] from trigger_plotOrthologs_together_with_estimatePeak_channel.merge(trigger_plotOrtholog_from_estimatePeak_channel)
          *    to be a trigger must be ["true", many true], so it must not contain string "false"
          *
-         * An accepted trigger comes from setupAdjustment if all ortholog data are already present and ready to be plotted; from estimatePeak together with wgdOrthologs 
+         * An accepted trigger comes from setupAdjustment if all ortholog data are already present and ready to be plotted; from estimatePeaks together with wgdOrthologs
          * when they have both finished with all the peaks; from setOrthologs and wgdOrthologs after this latter has done with all ortholog distributions;
-         * from setOrtholog and estimatePeak when all missing peaks are computed.
+         * from setOrtholog and estimatePeaks when all missing peaks are computed.
          */
 
     script:
-    if (LOG) {
-        log.info "Process plotOrthologDistrib (${task.index}) has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task, speciesLabel="", printIndex=true)
     """
-    echo "[$species] `date`"
-    echo "[$species] Plotting ortholog distributions"
+    echo ""
+    echo -n "`date "+%T"` Plotting ortholog distributions... "
 
     processDir=\$PWD
     cd $PWD
     echo "NF internal work directory for [plotOrthologDistrib] process:\n\$processDir\n" > $logs_folder/${logs_names["plotOrthologDistrib"]}
 
     ksrates plot-orthologs ${config} >> $logs_folder/${logs_names["plotOrthologDistrib"]} 2>&1
-
     RET_CODE=\$?
-    echo "[$species] Done [\${RET_CODE}]"
-    echo "[$species] log can be found in: $logs_folder/${logs_names["plotOrthologDistrib"]}"
-    echo "[$species] `date`"
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
+    echo "Log can be found in:"
+    echo " $logs_folder/${logs_names["plotOrthologDistrib"]}"
+
+    cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process plotOrthologDistrib terminates)
- */
-if (LOG) {
-    outplotOrthologDistrib
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[plotOrthologDistrib] " + it.replace('\n', '') 
-            } else {
-                "[plotOrthologDistrib] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outPlotOrthologDistrib, "plotOrthologDistrib")
 
 
 
@@ -660,35 +657,30 @@ process doRateAdjustment {
 
     input:
         val species from species_channel
-        val trigger from trigger_doRateCorrection_from_setParalog_channel.mix(trigger_doRateCorrection_from_estimatePeak_channel, trigger_doRateCorrection_from_wgdOrtholog_channel, trigger_doRateCorrection_from_wgdParalog_channel)
+        val trigger from trigger_doRateAdjustment_from_setParalog_channel.mix(trigger_doRateAdjustment_from_estimatePeak_channel, trigger_doRateAdjustment_from_wgdOrtholog_channel, trigger_doRateAdjustment_from_wgdParalog_channel)
         val logs_folder from logs_folder_channel
         file config from configfile
 
     output:
-        stdout outRateAdjustmentAnalysis
-        val true into trigger_peakCalling_from_doRateCorrection_channel
-        val true into trigger_drawTree_from_doRateCorrection_channel
+        stdout outDoRateAdjustment
+        val true into trigger_paralogsAnalyses_from_doRateAdjustment_channel
+        val true into trigger_drawTree_from_doRateAdjustment_channel
 
     when:
         trigger == "true" || trigger == true
         /*
          * String "true" comes from setParalog process, which returns either a string "true" or a string "false" (it uses "env" variable, not a boolean);
-         * Boolean true come from the other triggers, which return a boolean "val" true (trigger_doRateCorrection_from_estimatePeak_channel, trigger_doRateCorrection_from_wgdOrtholog_channel, trigger_doRateCorrection_from_wgdParalog_channel)
+         * Boolean true come from the other triggers, which return a boolean "val" true (trigger_doRateAdjustment_from_estimatePeak_channel, trigger_doRateAdjustment_from_wgdOrtholog_channel, trigger_doRateAdjustment_from_wgdParalog_channel)
          *
          * An accepted trigger can come from setParalog (if paralog data is already present it returns string "true", so that at least the paralog distribution will be plotted),
-         *     or from estimatePeak (updates the databases and sends a boolean true) or from wgdOrthologs (when finishes a single run returns boolean true) or finally
+         *     or from estimatePeaks (updates the databases and sends a boolean true) or from wgdOrthologs (when finishes a single run returns boolean true) or finally
          *     from wgdParalogs (when finishes returns boolean true).
          */
 
     script:
-    if (LOG) {
-        log.info "Process doRateAdjustment (${task.index}) will use species $species and has " +\
-                 "${task.cpus} ${ task.cpus == 1 ? 'CPU' : 'CPUs' } available."
-    }
+    logProcessInfo(task, speciesLabel="", printIndex=true)
     """
-    echo "[$species] `date`"
-    echo "[$species] Starting rate-adjustment analysis"
-
+    echo ""
     paranome=`grep "^[[:space:]]*paranome[[:space:]]*=" ${config} | cut -d "=" -f 2 | xargs | tr '[:upper:]' '[:lower:]'`
     colinearity=`grep "^[[:space:]]*collinearity[[:space:]]*=" ${config} | cut -d "=" -f 2 | xargs | tr '[:upper:]' '[:lower:]'`
 
@@ -701,64 +693,50 @@ process doRateAdjustment {
         missing_anchorpairs=true
     fi
 
-    if [ \${missing_paranome} = "true" ] && [ \${missing_anchorpairs} = "true" ]; then
-        echo "[$species] Whole-paranome and anchor pair data do not yet exist -> skipping rate-adjustment"
-    fi
-    if [ \${missing_paranome} = "true" ] && [ \${missing_anchorpairs} = "false" ]; then
-        echo "[$species] Whole-paranome data [${species}.ks.tsv] does not yet exist -> skipping rate-adjustment"
-    fi
-    if [ \${missing_paranome} = "false" ] && [ \${missing_anchorpairs} = "true" ]; then
-        echo "[$species] Anchor pair data [${species}.ks_anchors.tsv] does not yet exist -> skipping rate-adjustment"
+    if [ \${missing_paranome} = "true" ]; then
+        echo "Whole-paranome data not yet available; skipping rate-adjustment"
+        exit 0
     fi
-    if [ \${missing_paranome} = "true" ] || [ \${missing_anchorpairs} = "true" ]; then
-        echo "[$species] Done"
-        echo "[$species] `date`"
+    if [ \${missing_anchorpairs} = "true" ]; then
+        echo "Anchor-pair data not yet available; skipping rate-adjustment"
         exit 0
     fi
 
     processDir=\$PWD
     cd $PWD
-    
     echo "NF internal work directory for [doRateAdjustment (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
 
-    echo "[$species] Performing rate-adjustment"
+    echo -n "`date "+%T"` Starting rate-adjustment analysis... "
     ksrates orthologs-adjustment ${config} >> $logs_folder/${logs_names["doRateAdjustment"]} 2>&1
+    RET_CODE=\$?
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
     echo "\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
 
-    echo "[$species] Plotting mixed distributions"
+    echo -n "`date "+%T"` Plotting mixed distributions... "
     ksrates plot-paralogs ${config} >> $logs_folder/${logs_names["doRateAdjustment"]} 2>&1
-    echo "\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
+    RET_CODE=\$?
+    echo "done [\${RET_CODE}] `date "+%T"`"
 
-    echo " \n-----------------------------------------------------------\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
+    echo "\n-----------------------------------------------------------\n" >> $logs_folder/${logs_names["doRateAdjustment"]}
 
-    RET_CODE=\$?
-    echo "[$species] Done [\${RET_CODE}]"
-    echo "[$species] log can be found in: $logs_folder/${logs_names["doRateAdjustment"]}"
-    echo "[$species] `date`"
+    echo "Log can be found in:"
+    echo " $logs_folder/${logs_names["doRateAdjustment"]}"
+
+    cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process doRateAdjustment terminates)
- */
-if (LOG) {
-    outRateAdjustmentAnalysis
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[doRateAdjustment] " + it.replace('\n', '') 
-            } else {
-                "[doRateAdjustment] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outDoRateAdjustment, "doRateAdjustment")
 
 
 
 /*
  * Process that performs the WGM peak calling and generates the 
  * related figures (anchor pair Ks clustering and mixture model).
+ * It is performed only once as last process after all the doRateAdjustment's,
+ * when the adjustment table is certainly complete.
  */
 process paralogsAnalyses {
 
@@ -766,59 +744,44 @@ process paralogsAnalyses {
         val species from species_channel
         val logs_folder from logs_folder_channel
         file config from configfile
-        val trigger from trigger_peakCalling_from_doRateCorrection_channel.collect()
+        val trigger from trigger_paralogsAnalyses_from_doRateAdjustment_channel.collect()
 
     output:
-        stdout outPeakCalling
+        stdout outParalogsAnalyses
 
     script:
-    /*
-     * It is performed only once as last process after all the doRateAdjustment's,
-     * when the adjustment table is certainly complete.
-     */
+    logProcessInfo(task, species)
     """
-    echo "[$species] `date`"
-    echo "[$species] Performing WGM peak calling"
+    echo ""
+    echo -n "[$species] `date "+%T"` Starting detection of potential WGD signatures... "
 
     processDir=\$PWD
     cd $PWD
     echo "NF internal work directory for [paralogsAnalyses (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["paralogsAnalyses"]}
 
-    # If colinearity is on, perform peak calling only on anchor distribution with cluster-anchors
-    # Else, perform peak calling only on paranome with mixture model(s)
-    # Additional methods can be required through the expert configuration file
-
     ksrates paralogs-analyses ${config} >> $logs_folder/${logs_names["paralogsAnalyses"]} 2>&1
+    RET_CODE=\$?
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
     echo "\n" >> $logs_folder/${logs_names["paralogsAnalyses"]}
 
-    RET_CODE=\$?
-    echo "[$species] Done [\${RET_CODE}]"
-    echo "[$species] log can be found in: $logs_folder/${logs_names["paralogsAnalyses"]}"
-    echo "[$species] `date`"
+    echo "[$species] Log can be found in:"
+    echo "[$species]  $logs_folder/${logs_names["paralogsAnalyses"]}"
+
+    cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process paralogsAnalyses terminates)
- */
-if (LOG) {
-    outPeakCalling
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[paralogsAnalyses] " + it.replace('\n', '') 
-            } else {
-                "[paralogsAnalyses] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outParalogsAnalyses, "paralogsAnalyses")
 
 
 
 /*
  * Process that plots the input tree with branch length equal to 
  * the Ks distances.
+ * It is performed only once as last process after all the doRateAdjustment's,
+ * when the adjustment table is certainly complete.
  */
 process drawTree {
 
@@ -829,48 +792,34 @@ process drawTree {
         val species from species_channel
         val logs_folder from logs_folder_channel
         file config from configfile
-        val trigger from trigger_drawTree_from_doRateCorrection_channel.collect()
+        val trigger from trigger_drawTree_from_doRateAdjustment_channel.collect()
 
     output:
         stdout outDrawTree
 
     script:
-    /*
-     * It is performed only once as last process after all the doRateAdjustment's,
-     * when the adjustment table is certainly complete.
-     */
+    logProcessInfo(task)
     """
-    echo "[$species] `date`"
-    echo "[$species] Plotting tree with branch length equal to Ks distances"
+    echo ""
+    echo -n "`date "+%T"` Plotting phylogram with Ks branch lengths... "
 
     processDir=\$PWD
     cd $PWD
-    echo "NF internal work directory for [drawTree (${task.index})] process:\n\$processDir\n" >> $logs_folder/${logs_names["drawTree"]}
+    echo "NF internal work directory for [drawTree] process:\n\$processDir\n" >> $logs_folder/${logs_names["drawTree"]}
 
     ksrates plot-tree ${config} --nextflow >> $logs_folder/${logs_names["drawTree"]} 2>&1
-
     RET_CODE=\$?
-    echo "[$species] Done [\${RET_CODE}]"
-    echo "[$species] log can be found in: $logs_folder/${logs_names["drawTree"]}"
-    echo "[$species] `date`"
+    echo "done [\${RET_CODE}] `date "+%T"`"
+
+    echo "Log can be found in:"
+    echo " $logs_folder/${logs_names["drawTree"]}"
+
+    cd \$processDir
     """
 }
 
-/*
- * Log output to stdout/console.
- * (output will be logged only after process drawTree terminates)
- */
-if (LOG) {
-    outDrawTree
-        .splitText() { 
-            if ( it.endsWith("\n") ) {
-                "[drawTree] " + it.replace('\n', '') 
-            } else {
-                "[drawTree] $it" 
-            }
-        }
-        .subscribe { log.info it }
-}
+// Log output to stdout/console.
+logProcessOutput(outDrawTree, "drawTree")
 
 
 
@@ -878,11 +827,12 @@ if (LOG) {
  * On completion of workflow clean up any temporary files left behind.
  */
 workflow.onComplete {
-    if (LOG) {
+    if (LOG_OUTPUT) {
         log.info ""
-        log.info("Logs folder: logs_${workflow.sessionId.toString().substring(0,8)}")
-
-        if ( params.preserve == false ) {
+        log.info ""
+        // if a ksrates config file needed to be generated (newConfigFile == true,
+        // see also process checkConfig) then there won't be anything to clean up
+        if ( params.preserve == false && !newConfigFile) {
             log.info "Cleaning up any temporary files left behind..."
 
             focal_species_line = file("${configfile}").readLines().find{ it =~ /focal_species/ }
@@ -949,13 +899,15 @@ workflow.onComplete {
                     }
                 }
 
-            log.info "Done."
+            log.info "Done"
             log.info ""
         }
 
+        log.info "Logs folder: logs_${workflow.sessionId.toString().substring(0,8)}"
+        log.info ""
         log.info "Pipeline completed at: $workflow.complete taking $workflow.duration"
         log.info "Execution status: ${ workflow.success ? 'OK' : 'failed' }"
-        log.info ""
+//        log.info ""
 //        log.info "Project:    $workflow.projectDir"
 //        log.info "Cmd line:   $workflow.commandLine"
 //        log.info "Session ID: $workflow.sessionId"
@@ -974,6 +926,7 @@ workflow.onError {
     // If user interrupts with ctrl+C
     if ( workflow.errorReport == "SIGINT" || workflow.errorMessage == "SIGINT" ) {
         error_box_sigint = "Pipeline interrupted by user (${workflow.errorMessage} signal)"
+        log.error " "
         log.error "${'=' * error_box_sigint.length()}\n" + \
                   "${error_box_sigint}\n" + \
                   "${'=' * error_box_sigint.length()}"
@@ -1025,7 +978,9 @@ workflow.onError {
         }
 
         // Define the stopped process log filename
-        log_filename = "rate_adjustment/${focal_species}/logs_${workflow.sessionId.toString().substring(0,8)}/${logs_names[process]}"
+        focal_species_dir = focal_species != "" ? "${focal_species}/" : ""
+        log_filename = "rate_adjustment/${focal_species_dir}" + \
+                       "logs_${workflow.sessionId.toString().substring(0,8)}/${logs_names[process]}"
 
         // Parse the "Caused by:" line from errorReport
         // Find in errorReport the line matching "Caused by:" and get its index
@@ -1067,8 +1022,9 @@ workflow.onError {
                 }
 
                 // Point to errorReport and to the complete output of the stopped process log file
-                error_box += "\nMore details can be found in the error report above or in the following log file:\n" + \
-                             "${log_filename}\n"
+                error_box += "\nMore details may be found in the error report above, in ./.nextflow.log, " + \
+                             "and/or in the \n" + \
+                             "following log file: ${log_filename}\n"
             }
         }
 
@@ -1085,18 +1041,19 @@ workflow.onError {
 
             // Point to the complete Nextflow errorReport, to nextflow.log (and to the wgd_ortholog_ log file)
             if ( unknown_species_pair == false ) {
-                error_box += "\nMore details may be found in the error report above or in ./.nextflow.log.\n"
+                error_box += "\nMore details may be found in the error report above and/or in ./.nextflow.log\n"
             }
             else {
-                error_box += "\nMore details may be found in the error report above, in ./.nextflow.log, or in one of\n" + \
+                error_box += "\nMore details may be found in the error report above, in ./.nextflow.log, and/or in one of\n" + \
                              "the log files named rate_adjustment/${focal_species}/" + \
-                             "logs_${workflow.sessionId.toString().substring(0,8)}/${logs_names["wgdOrthologs"]} (if any exists).\n"
+                             "logs_${workflow.sessionId.toString().substring(0,8)}/${logs_names["wgdOrthologs"]} (if any exist)\n"
             }
         }
 
         // Separator to highlight the end of the error box
         error_box += "${'=' * headline.length()}"
 
+        log.error " "
         log.error "${error_box}"
     }
 }
diff --git a/test/nextflow.config b/test/nextflow.config
index 96863ca..8af67c5 100644
--- a/test/nextflow.config
+++ b/test/nextflow.config
@@ -37,7 +37,7 @@ process {
         // clusterOptions = ''     // e.g. '-l h_vmem=2G'
     }
 
-    // withName: 'estimatePeak' {
+    // withName: 'estimatePeaks' {
     //     memory = ''             // e.g. '2GB'
     //     clusterOptions = ''     // e.g. '-l h_vmem=2G'
     // }