Merge pull request #49 from UPHL-BioNGS/refactoring

Refactoring to one file

.github/workflows/github_actions.config

@@ -1,57 +1,111 @@
 process {
-  withName:unicycler{
-    cpus = 2
-  }
-  withName:flye{
-    cpus = 2
-  }
-  withName:dragonflye{
-    cpus = 2
-  }
-  withName:masurca{
-    cpus = 2
-  }
-  withName:medaka{
-    cpus = 2
-  }
-  withName:nanoplot{
-    cpus = 2
-  }
-  withName:miniasm{
-    cpus = 2
-  }
-  withName:porechop{
-    cpus = 2
-  }
-  withName:rasusa{
-    cpus = 2
-  }
-  withName:raven{
-    cpus = 2
-  }
-  withName:'trycycler.*'{
-    cpus = 2
-  }
-  withName:cluster {
-    cpus = 2
-  }
-  withName:reconcile{
-    cpus = 2
-    errorStrategy = 'ignore'
-  }
-  withName:msa {
-    cpus = 2
-  } 
-  withName:partition {
-    cpus = 2
-  }
-  withName:consensus {
-    cpus = 2
-  } 
-  withName:combine {
-    cpus = 2
-  } 
-  withName:unicycler {
-    cpus = 2
-  } 
+	maxForks = 1
+
+	withName:bandage{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:busco{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:bwa{
+		cpus=3
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:circulocov{
+		cpus=3
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:copy{
+		cpus=2
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:dnaapler{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:fastp{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:flye{
+		cpus=3
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:gfastats{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:gfa_to_fasta{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:medaka{
+		cpus=3
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:multiqc{
+		cpus=3
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:nanoplot_summary{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:nanoplot{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:polypolish{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:pypolca{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:rasusa{
+		cpus=2
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:raven{
+		cpus=2
+		ext.args = ' '
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'ignore'}
+	}
+	withName:summary{
+		cpus=2
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:unicycler{
+		cpus=3
+		memory = { 6.GB * task.attempt }
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:versions{
+		cpus=2
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:test{
+		cpus=2
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
 }

.github/workflows/github_actions_hybrid_sample_sheet.txt

@@ -1,2 +1,2 @@
 sample,fastq,fastq_1,fastq_2
-test,long_reads_low_depth.fastq.gz,short_reads_1.fastq.gz,short_reads_2.fastq.gz
+test,reads/long_reads_low_depth.fastq.gz,reads/short_reads_1.fastq.gz,reads/short_reads_2.fastq.gz