slurp bash code into python

pipes/WDL/tasks/tasks_ncbi.wdl

@@ -735,7 +735,8 @@ task biosample_to_genbank {
  out_headers.append('note')
  outf_smt.write('\t'.join(out_headers)+'\n')
 
- with open("~{base}.biosample.map.txt", 'wt') as outf_biosample:
+ with open("~{base}.sample_ids.txt", 'wt') as outf_ids:
+ with open("~{base}.biosample.map.txt", 'wt') as outf_biosample:
  outf_biosample.write('BioSample\tsample\n')
 
  for row in biosample_attributes:
@@ -777,16 +778,17 @@ task biosample_to_genbank {
 
  # write entry for this sample
  outf_smt.write('\t'.join(outrow[h] for h in out_headers)+'\n')
+ outf_ids.write(outrow['Sequence_ID']+'\n')
 
  # also write numbered versions for every segment/chromosome
  sample_name = outrow['Sequence_ID']
  if ~{num_segments}>1:
  for i in range(~{num_segments}):
  outrow['Sequence_ID'] = "{}-{}".format(sample_name, i+1)
  outf_smt.write('\t'.join(outrow[h] for h in out_headers)+'\n')
+ outf_ids.write(outrow['Sequence_ID']+'\n')
 
  CODE
- cut -f 1 "${base}.genbank.src" | tail +2 > "${base}.sample_ids.txt"
  >>>
  output {
  File genbank_source_modifier_table = "~{base}.genbank.src"