Genomics in the Cloud by Geraldine A. Van der Auwera

Author:Geraldine A. Van der Auwera
Language: eng
Format: epub
Publisher: O'Reilly Media
Published: 2020-04-09T00:00:00+00:00

How is the conditional logic set up?

In the match-up diagram in Table 9-1, we saw the box showing the call to CramToBamTask under the control of the presumed conditional switch. We identified the corresponding code by searching for call CramToBamTask and capturing the lines around it that are likely to be involved:

if ( is_cram ) { call CramToBamTask { input: input_cram = input_bam, ... } }

You can read this snippet of code as “If the is_cram condition is verified, call CramToBamTask and give it whatever was provided as input_bam.” This immediately brings up two important questions: how are we testing for that initial condition, and how are we handling the apparent contradiction in the input_cram = input_bam input assignment?

Let’s tackle the first question by scrolling up a bit in the workflow code until we find a reference to this mysterious is_cram variable. And here it is on line 59:

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