Allow minimap's -f parameter to be set

From minimap2's --help:

-f FLOAT     filter out top FLOAT fraction of repetitive minimizers [0.0002]

Setting this higher allows us to handle input references with large
numbers of repetitive sequences.

Also bump up minimap2 memory/cpu resources on milton.

.test/test.config

@@ -44,6 +44,11 @@ params {
 
  // count partially mapped reads
  lenient_counts = false
+
+ // minimap -f parameter (filter out fraction or number of repetitive minimisers)
+ // set this to a higher value if using a reference with a large number of
+ // repetitive sequences
+ minimap_f = 0.0002
 }
 
 //SQL DB Plugin

modules/count.nf

@@ -43,6 +43,7 @@ process CountGuides {
  script:
  def outCounts = "${sampleName}_guide_counts.txt"
  def lenientFlag = params.lenient_counts ? "--lenient" : ""
+ def extraThreads = task.cpus - 1
  /*
  count collation is a hacky bash script to get collated output,
  the script pastes the count files together, and then cuts out
@@ -54,10 +55,10 @@ process CountGuides {
  do
  sample=\${fastq%.fastq*}
 
- minimap2 -ax map-ont -N 1 \
+ minimap2 -ax map-ont -N 1 -t ${task.cpus} -f ${params.minimap_f} \
  ${guides_index} \$fastq | \
- samtools view -S -b | \
- samtools sort -o \${sample}.bam
+ samtools view -S -b -@ ${extraThreads} | \
+ samtools sort -@ ${extraThreads} -o \${sample}.bam
 
  count_guides.py \${sample}.bam ${params.guides_fasta} ${lenientFlag} > \${sample}_counts.txt
  done

nextflow.config

@@ -44,6 +44,11 @@ params {
 
  // count partially mapped reads
  lenient_counts = false
+
+ // minimap -f parameter (filter out fraction or number of repetitive minimisers)
+ // set this to a higher value if using a reference with a large number of
+ // repetitive sequences
+ minimap_f = 0.0002
 }
 
 //SQL DB Plugin
@@ -73,10 +78,14 @@ profiles {
  memory = { 8.GB * task.attempt }
  time = '12h'
  errorStrategy = { 'retry' }
- maxRetries = 4
+ maxRetries = 3
  withLabel:SplitCode {
  module = 'splitcode/0.28.3'
  }
+ withLabel:CountGuides {
+ cpus = 8
+ memory = { 64.GB * task.attempt }
+ }
  }
  }
  test {

nextflow_schema.json

@@ -154,6 +154,12 @@
  "fa_icon": "fas fa-cog",
  "default": "",
  "hidden": true
+ },
+ "minimap_f": {
+ "type": "float",
+ "default": 0.002,
+ "description": "Minimap2 -f parameter (default = 0.002). Set this higher for highly repetitive sequences. Accepts integer threshold or fraction.",
+ "hidden": true
  }
  }
  }