Expose low depth cutoff parameter

Edinburgh-Genome-Foundry · Aug 22, 2023 · b7b972f · b7b972f
1 parent cbd1fc4
commit b7b972f
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/bin/analysis.py b/bin/analysis.py
@@ -15,6 +15,7 @@
 params_projectname = sys.argv[2]
 pdf_file = sys.argv[3]
 results_csv_file = sys.argv[4]
+low_depth_value = sys.argv[5]
 
 import pandas as pd
 from Bio import SeqIO
@@ -75,7 +76,8 @@
 
 
 # Create PDF report
-sequencinggroup = edi.SequencingGroup(comparatorgroups, name=params_projectname)
+sequencinggroup = edi.SequencingGroup(comparatorgroups, name=params_projectname,
+ low_depth_cutoff=low_depth_value)
 sequencinggroup.perform_all_comparisons_in_sequencinggroup()
 edi.write_sequencinggroup_report(target=pdf_file, sequencinggroup=sequencinggroup)
 

diff --git a/nextflow.config b/nextflow.config
@@ -14,6 +14,7 @@ params {
  quality_cutoff = 10 // For NanoFilt
  min_length = 500 // nucleotides
  freebayes.args = '--ploidy 1 --min-alternate-fraction 0.1 --min-alternate-count 2 --min-base-quality 20'
+ low_depth_value = 30 // cutoff for low-depth samples
 
 
  // Review pipeline

diff --git a/nextflow/sequeduct_analysis.nf b/nextflow/sequeduct_analysis.nf
@@ -167,7 +167,7 @@ process runEdiacara {
  pdf_file = "Ediacara_report.pdf"
  results_csv_file = "results.csv"
  """
- analysis.py $samplesheet_csv "$params.projectname" $pdf_file $results_csv_file
+ analysis.py $samplesheet_csv "$params.projectname" $pdf_file $results_csv_file $params.low_depth_value
  """
 }