code: def test_process_somatic(
      self, model_type, use_slim_model, process_somatic
  ):
      FLAGS.model_type = model_type
      FLAGS.ref = "your_ref"
      FLAGS.reads_tumor = "your_tumor_bam"
      FLAGS.reads_normal = "your_normal_bam"
      FLAGS.output_vcf = "your_vcf"
      FLAGS.output_gvcf = "your_gvcf"
      FLAGS.num_shards = 64
      FLAGS.customized_model = "/opt/models/wgs/model.ckpt"
      FLAGS.use_slim_model = use_slim_model
      FLAGS.process_somatic = process_somatic
      commands = run_deepsomatic.create_all_commands_and_logfiles(
          "/tmp/deepsomatic_tmp_output", used_in_test=True
      )
  
      extra_args_plus_gvcf = (
          '--gvcf "/tmp/deepsomatic_tmp_output/gvcf.tfrecord@64.gz"'
      )
  
      self.assertEqual(
          commands[0][0],
          "time seq 0 63 | parallel -q --halt 2 --line-buffer"
          " /opt/deepvariant/bin/make_examples_somatic --mode calling --ref"
          ' "your_ref" --reads_tumor "your_tumor_bam" --reads_normal'
          ' "your_normal_bam" --examples'
          ' "/tmp/deepsomatic_tmp_output/make_examples_somatic.tfrecord@64.gz"'
          ' --channels "insert_size"'
          " %s"
          ' --vsc_max_fraction_indels_for_non_target_sample "0.5"'
          ' --vsc_max_fraction_snps_for_non_target_sample "0.5"'
          ' --vsc_min_fraction_indels "0.05" --vsc_min_fraction_snps "0.029"'
          " --task {}" % (extra_args_plus_gvcf),
      )
      call_variants_bin = (
          "call_variants_slim" if use_slim_model else "call_variants"
      )
      self.assertEqual(
          commands[1][0],
          "time /opt/deepvariant/bin/{} --outfile"
          ' "/tmp/deepsomatic_tmp_output/call_variants_output.tfrecord.gz"'
          " --examples"
          ' "/tmp/deepsomatic_tmp_output/make_examples_somatic.tfrecord@64.gz"'
          ' --checkpoint "/opt/models/{}/model.ckpt"'.format(
              call_variants_bin, model_type.lower()
          ),
      )
      if process_somatic:
          self.assertEqual(
              commands[2][0],
              (
                  "time /opt/deepvariant/bin/postprocess_variants "
                  '--ref "your_ref" '
                  "--infile "
                  '"/tmp/deepsomatic_tmp_output/call_variants_output.tfrecord.gz" '
                  '--outfile "your_vcf" '
                  "--cpus 0 "
                  "--process_somatic=true "
                  '--gvcf_outfile "your_gvcf" '
                  "--nonvariant_site_tfrecord_path "
                  '"/tmp/deepsomatic_tmp_output/gvcf.tfrecord@64.gz"'
              ),
          )
      else:
          self.assertEqual(
              commands[2][0],
              (
                  "time /opt/deepvariant/bin/postprocess_variants "
                  '--ref "your_ref" '
                  "--infile "
                  '"/tmp/deepsomatic_tmp_output/call_variants_output.tfrecord.gz" '
                  '--outfile "your_vcf" '
                  "--cpus 0 "
                  "--noprocess_somatic "
                  '--gvcf_outfile "your_gvcf" '
                  "--nonvariant_site_tfrecord_path "
                  '"/tmp/deepsomatic_tmp_output/gvcf.tfrecord@64.gz"'
              ),
          )
  
file_path: deepvariant/scripts/run_deepsomatic_test.py
imports: from absl import flags
  from absl.testing import absltest
  from absl.testing import flagsaver
  from absl.testing import parameterized
  from deepvariant.opensource_only.scripts import run_deepsomatic
label_desc: Use image node_id 2 for calling the RunDeepSomaticTest obj's underlying member method code with example usage: obj.test_process_somatic(model_type, use_slim_model, process_somatic) without return types