Merge branch 'main' into dev

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) matthew wells
+Copyright (c) 2023 Public Health Agency of Canada
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -16,6 +16,7 @@ Mikrokondo takes in either, Illumina, Nanopore or Pacbio data (Pacbio data only
 
 # Installation
 
+
 ## Installing Nextflow
 Nextflow is required to run mikrokondo, but fortunately it is not too hard to install (Linux is required). The instructions for installing Nextflow can be found at either either resource: [Nextflow Home](https://www.nextflow.io/) or  [Nextflow Documentation](https://www.nextflow.io/docs/latest/getstarted.html#installation)
 

conf/modules.config

@@ -266,8 +266,10 @@ process {
 
     withName: MASH_ESTIMATE {
         //container = params.mash.container
+        errorStrategy = { task.attempt <= task.maxRetries ? sleep(Math.pow(2, task.attempt) * 200 as long) && 'retry' : 'finish' }
         ext.containers = params.mash
         scratch = false
+        maxForks = 20
         stageInMode = params.stage_in_mode
             publishDir = [
                 [
@@ -322,7 +324,7 @@ process {
     withName: MASH_SCREEN {
         def dir_out = null
         //errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
-        errorStrategy = 'ignore'
+        errorStrategy = { task.attempt <= task.maxRetries ? sleep(Math.pow(2, task.attempt) * 200 as long) && 'retry' : 'finish' }
         maxForks = 20
         //dir_out =  process.toString().contains("QC_READS") ? "read_quality/${params.mash.output_dir}/mash" : "taxon_determination/mash"
         ext.args = "-w"

nextflow.config

@@ -94,8 +94,10 @@ params {
     validate_params            = true
     show_hidden_params         = false
 
+
     // If a param in camel case is present nextflow automatically creates a kebab case parameter as well
     schema_ignore_params       = 'genomes,flye_read_type,shigeifinder,lissero,sistr,ectyper,bandage,bakta,unicycler,medaka,pilon_iterative,pilon,racon,samtools,minimap2,r_contaminants,mash,kraken,checkm,quast_filter,quast,fastqc,spades,flye,chopper,fastp,seqtk,kat,coreutils,opt_platforms,QCReportFields,QCReport-fields,QCReport,kraken_bin,shigatyper,spatyper,kleborate,subtyping_report,kraken_species,top_hit_species,mash_meta,mlst,raw_reads,abricate_params,target_depth'
+
     stage_in_mode = 'symlink'
 
 
@@ -195,6 +197,7 @@ params {
     }
 
     // Flye options
+    // TODO figure out if --keep-haplotypes should be enabled
     flye {
         // TODO add in arg for data type in flye
         nanopore {