update docs/assets

docs/assets/defaults.config

@@ -56,14 +56,16 @@ params {
 
 // Select the appropriate shasta config to use for assembly
 // Since shasta v0.8 (Oct/2021) this parameter is now mandatory.
+// You can check availability at: https://paoloshasta.github.io/shasta/Configurations.html
   shasta_config = "Nanopore-Oct2021"
 
 // Tells the pipeline to interpret the long reads as "corrected" long reads.
-// This will activate (if available) the options for corrected reads in the
-// assemblers: -corrected (in canu), --pacbio-corr|--nano-corr (in flye), etc.
-// Be cautious when using this parameter. If your reads are not corrected, and
+// This will activate (if available) the options for corrected or even high
+// quality (hq) reads in the assemblers.
+// Be cautious when using this parameter. If your reads are not corrected|hq, and
 // you use this parameter, you will probably do not generate any contig.
-  corrected_long_reads = false
+  corrected_longreads    = false
+  high_quality_longreads = false
 
 // This parameter below (hybrid_strategy) is to select the hybrid strategies adopted by the pipeline.
 // Read the documentation https://mpgap.readthedocs.io/en/latest/manual.html to know more about the hybrid strategies.
@@ -132,10 +134,32 @@ params {
   skip_shasta    = false                      // Nanopore longreads only assemblies
   shasta_additional_parameters = null         // Must be given as shown in shasta manual. E.g. " --Reads.minReadLength 5000 "
 
-// Max resource options
-// Defaults only, expecting to be overwritten
-  max_memory                 = '14.GB'
-  max_cpus                   = 6
+
+            /*
+             * Resources controlling parameters
+             * 
+             * Here some parameters that allow the user to better tune the resources used by the pipeline.
+             *
+             * The start_asm_{mem,cpus} parameter tells the pipeline how much memory should the assembly
+             * modules and quast request in the first try. This is essential for bigger genomes in order
+             * to avoid having to fail the first try due lack of memory and then running again (automatically)
+             * using all the max values allowed with the max_{mem,cpus} parameters.
+             *
+             * The max_memory and max_cpus parameters, tell the pipeline how much is the maximum number of
+             * these items that is allowoed per job. The pipeline start by requesting less mem&cpus than 
+             * what is defined by these params, and, in case the first try fails, it then maxes out the job
+             * to use the maximum number you allowed.
+             *
+             * The max_time parameter defines how long a single job is allowed to run.
+             */
+
+  // starting values for the assembly jobs (and quast) to ask for in the very first try
+  start_asm_mem              = 20.GB
+  start_asm_cpus             = 6
+
+  // maximum values to be used on automatic second try in case of lack of memory (all jobs)
+  max_memory                 = 40.GB
+  max_cpus                   = 10
   max_time                   = '40.h'
 
 }