Add a new sample to the SMC-DNA challenge

smc_add_new_sample.py

## SMC-DNA challenges are configured by entries in the table smc-dna-config,
## which lives in the MutationCallingChallengeStaging project, here:
## https://www.synapse.org/#!Synapse:syn4686078

## To add a new sample:


## create new evaluation queue (one for each of SNV, SV and possibly indel)
evaluation_snv = syn.store(Evaluation(
    name="synthetic.challenge.set6.snv",
    description="ICGC-TCGA Mutation Calling Challenge - synthetic tumor 6",
    contentSource="syn2177211"))

## you've uploaded a truth vcf file to a non-public folder, right?
truth = syn.get(...TRUTH_FILE_SYN_ID...)

## each row of the smc-dna-config table configures one evaluation queue
new_rows = [[
    evaluation_snv.id,           ## Eval_id
    truth.id,                    ## Truth_id
    "synthetic_6",               ## Tumor
    "snv",                       ## Mode
    "Synthetic 6 SNV",           ## Title
    "Mask",                      ## Score_columns
    "2016-01-31 00:00:00",       ## Deadline
    "evaluator"                  ## Eval_code
]]

## get smc-dna-config table's schema:
schema = syn.get('syn4686078')

## upload the rows to Synapse
table = syn.store(Table(schema, new_rows))

This is a template. This code will not work as is, but should be used in an interactive Python session to create the needed artifacts - evaluation queues and entries in the configuration table.