Factor out Python script in review pipeline

nextflow/sequeduct_review.nf

@@ -140,32 +140,7 @@ process trimAssembly {
  script:
  trimmed_denovo = barcode + '_denovo.fasta'
  """
- #!/usr/bin/env python
- from Bio import SeqIO
-
- canu_fasta = "$assembly_dir" + '/' + "$params.assembly_prefix" + "$params.canu_postfix"
- try:
- contig = SeqIO.read(canu_fasta, format="fasta")
- except:
- print("The FASTA file contains more than 1 contigs. First contig used.")
- contig = next(SeqIO.parse(canu_fasta, format="fasta"))
-
- entries = contig.description.split(" ")
- desc_dict = {"name": entries[0]} # first is the name
- for entry in entries[1:]: # addressed the first one above
- elements = entry.split("=")
- desc_dict[elements[0]] = elements[1]
-
- # canu assembly: 0-based, from-index inclusive, end-index exclusive
- if desc_dict["suggestCircular"] == "yes": # as output by canu
- start, end = desc_dict["trim"].split("-") # must contain 2 values
- start = int(start)
- end = int(end)
- SeqIO.write(contig[start:end], "$trimmed_denovo", format="fasta")
- else: # keep intact
- SeqIO.write(contig, "$trimmed_denovo", format="fasta")
- 
- print("Trimmed:", "$barcode")
+ trim_assembly.py "$assembly_dir" "$params.assembly_prefix" "$params.canu_postfix" "$trimmed_denovo" "$barcode"
  """
 }