Read genomeSize from csv

Edinburgh-Genome-Foundry · Sep 1, 2022 · 6c7552e · 6c7552e
1 parent ade9b0d
commit 6c7552e
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/main.nf b/main.nf
@@ -102,8 +102,9 @@ workflow assembly {
 
  .map { row -> 
  def barcode = row['Barcode'] // a barcode is present only once -- no pooling
+ def length = row['Length'] // estimated length in kbp for canu genomeSize parameter
  def fastq_path = file("${params.fastq_filtered_dir}/${barcode}.fastq")
- return [barcode, fastq_path]
+ return [barcode, fastq_path, length]
  }
  .set { entries_assembly_ch }
 

diff --git a/nextflow/sequeduct_review.nf b/nextflow/sequeduct_review.nf
@@ -216,13 +216,12 @@ process assembleOnly {
  publishDir 'results/dir4_assembly/n1_de_novo_assembly', mode: 'copy'
 
  input:
- tuple val(barcode), path(fastq_path)
+ tuple val(barcode), path(fastq_path), val(length)
  output:
  tuple val(barcode), path(assembly_dir)
  script:
  assembly_dir = barcode + '_assembly'
- // genomsize_param = 'genomeSize=' + seq_length + 'k'
- genomsize_param = 'genomeSize=8k'
+ genomsize_param = 'genomeSize=' + length + 'k'
  """
  canu -p $params.assembly_prefix -d $assembly_dir $genomsize_param -nanopore $fastq_path
  """