PR for release

.github/workflows/github_actions.config

@@ -3,22 +3,22 @@ process {
 
 	withName:bandage{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:busco{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:bwa{
 		cpus=3
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:circulocov{
 		cpus=3
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:copy{
@@ -27,68 +27,73 @@ process {
 	}
 	withName:dnaapler{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:fastp{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:flye{
 		cpus=3
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:gfastats{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:gfa_to_fasta{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mash{
+		cpus=3
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:medaka{
 		cpus=3
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:multiqc{
 		cpus=3
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:nanoplot_summary{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:nanoplot{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:polypolish{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:pypolca{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:rasusa{
 		cpus=2
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:raven{
 		cpus=2
 		ext.args = ' '
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'ignore'}
 	}
 	withName:summary{
@@ -97,7 +102,7 @@ process {
 	}
 	withName:unicycler{
 		cpus=3
-		memory = { 6.GB * task.attempt }
+		memory = { 6.GB  }
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 	withName:versions{

README.md

@@ -27,6 +27,7 @@ We made a [wiki](https://github.com/UPHL-BioNGS/Donut_Falls/wiki), please read i
   - [Examples](https://github.com/UPHL-BioNGS/Donut_Falls/wiki/Usage#examples)
   - [Using as a subworkflow](https://github.com/UPHL-BioNGS/Donut_Falls/wiki/Linking)
 - [Workflow DAG](https://github.com/UPHL-BioNGS/Donut_Falls/wiki#basic-diagram-of-the-workflow-and-subworkflows)
+- [Assessing Assembly Quality](https://github.com/UPHL-BioNGS/Donut_Falls/wiki/evaluation)
 - [FAQ](https://github.com/UPHL-BioNGS/Donut_Falls/wiki/FAQ)
 
 ## Getting started
@@ -117,5 +118,5 @@ Donut Falls would not be possible without
 - [polypolish](https://github.com/rrwick/Polypolish) : reduces sequencing artefacts through polishing with Illumina reads
 - [pypolca](https://github.com/gbouras13/pypolca) : reduces sequencing artefacts through polishing with Illumina reads
 - [rasusa](https://github.com/mbhall88/rasusa) : subsampling nanopore reads to 150X depth
-- [raven](https://github.com/lbcb-sci/raven) : de novo assembly option (params.assembler = 'miniasm')
+- [raven](https://github.com/lbcb-sci/raven) : de novo assembly option (params.assembler = 'raven')
 - [unicycler](https://github.com/rrwick/Unicycler) : hybrid assembly option (params.assembler = 'unicycler')