From 8ae99e40bc6fd82be4651989f33102bc2614ae51 Mon Sep 17 00:00:00 2001 From: Tavi Nathanson Date: Thu, 11 May 2017 21:58:44 +0000 Subject: [PATCH] Add example #6 to README --- README.md | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 4255388..f3ef574 100644 --- a/README.md +++ b/README.md @@ -22,14 +22,14 @@ cohort.add_epidisco_pipeline( cohort.add_epidisco_pipeline( pipeline_name="epidisco_2", config=EpidiscoConfig(cohort, - arg_normal_input=lambda patient: patient.tumor_sample.bam_path_dna)) + arg_normal_input=lambda patient: patient.normal_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)) + arg_normal_input=lambda patient: patient.normal_sample.bam_path_dna)) # Customize the normal BAM input, the run name, and which patients to run on. cohort.add_epidisco_pipeline( @@ -37,7 +37,7 @@ cohort.add_epidisco_pipeline( 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)) + arg_normal_input=lambda patient: patient.normal_sample.bam_path_dna)) # Same as #4, but written differently. class EpidiscoConfigModified(EpidiscoConfig): @@ -49,6 +49,12 @@ modified_config = EpidiscoConfigModified(cohort) cohort.add_epidisco_pipeline( pipeline_name="epidisco_5", config=modified_config) + +# Customize any CLI argument; for example, picard_java_max_heap_size. +cohort.add_epidisco_pipeline( + pipeline_name="epidisco_6", + config=EpidiscoConfig(cohort, + arg_picard_java_max_heap_size="20g")) # This is Discohort's own dry run functionality, FYI. Should have a better name. cohort.run_pipeline("epidisco_1", dry_run=True)