Update README

README.md

@@ -4,11 +4,52 @@ Generate Cohorts based on Epidisco and/or Biokepi results
 ## Example Usage
 
 ```
+from utils.data import load_cohort
 from discohorts import Discohort
-cohort = Discohort(cohort)
-cohort.add_pipeline(name="dna_processing",
-                    ocaml_path="dna_processing.ml",
-                    other_cli_args={"reference-build": "b37decoy",
-                                    "bam-path": lambda patient: patient.tumor_sample.bam_path_dna})
-cohort.run_pipeline("dna_processing")
+
+cohort = load_cohort(min_tumor_mtc=0, min_normal_mtc=0)
+work_dirs = ["/nfs-pool-{}/biokepi/".format(i) for i in range(2, 17)]
+dest_results_dir = "/nfs-pool/biokepi/results"
+cohort = Discohort(
+    cohort,
+    biokepi_work_dirs=work_dirs,
+    dest_results_dir=dest_results_dir)
+
+cohort.add_epidisco_pipeline(
+    pipeline_name="epidisco_1")
+
+# Customize the normal BAM input.
+cohort.add_epidisco_pipeline(
+    pipeline_name="epidisco_2",
+    config=EpidiscoConfig(cohort,
+                          arg_normal_input=lambda patient: patient.tumor_sample.bam_path_dna))
+
+# Customize the normal BAM input and the run name.
+cohort.add_epidisco_pipeline(
+    pipeline_name="epidisco_3",
+    run_name=lambda patient: "epidisco_{}".format(patient.id),
+    config=EpidiscoConfig(cohort,
+                          arg_normal_input=lambda patient: patient.tumor_sample.bam_path_dna))
+
+# Customize the normal BAM input, the run name, and which patients to run on.
+cohort.add_epidisco_pipeline(
+    pipeline_name="epidisco_4",
+    run_name=lambda patient: "epidisco_{}".format(patient.id),
+    config=EpidiscoConfig(cohort,
+                          keep=lambda patient: patient.id == "468",
+                          arg_normal_input=lambda patient: patient.tumor_sample.bam_path_dna))
+
+# Same as #4, but written differently.
+class EpidiscoConfigModified(EpidiscoConfig):
+    def keep(self, patient):
+        return patient.id == "468"
+    def arg_normal_input(self, patient):
+        return patient.tumor_sample.bam_path_dna
+modified_config = EpidiscoConfigModified(cohort)
+cohort.add_epidisco_pipeline(
+    pipeline_name="epidisco_5",
+    config=modified_config)
+
+# This is Discohort's own dry run functionality, FYI. Should have a better name.
+cohort.run_pipeline("epidisco_1", dry_run=True)
 ```