wrapper_example.wdl

version 1.0

import "https://raw.githubusercontent.com/aofarrel/myco/main/myco_simple.wdl" as main

# This is just a one-sample wrapper for myco_simple. It is intended for Terra data tables with a format like this:
#
#  | entity:sample_id | FASTQ_forward             | FASTQ_reverse             | decontaminated_fastq_1 | decontaminated_fastq_2 |
#  |------------------|---------------------------|---------------------------|------------------------|------------------------|
#  | sampleA          | raw_A_r1.fq               | raw_A_r2.fq               | decontam_A_r1.fq       | decontam_A_r2.fq       |
#  | sampleB          | raw_B1_r1.fq, rawB2_r1.fq | raw_B1_r2.fq, rawB2_r2.fq | decontam_B_r1.fq       | decontam_B_r2.fq       |
#  | sampleC          | raw_C_r1.fq               | raw_C_r2.fq               | decontam_C_r1.fq       | decontam_C_r2.fq       |
#
# However, you don't need to use this wrapper at all. You could still use the above Terra data table with myco_simple 
# 

workflow myco_simple_one_sample {
    input {
        File decontaminated_fastq_1
        File decontaminated_fastq_2
    }

    call main.myco {
        input:
            paired_decontaminated_fastq_sets = [[decontaminated_fastq_1, decontaminated_fastq_2]]
    }

output {
		Array[File] vcfs = myco.vcfs
		Array[File] masks = myco.masks
		Array[File?] diffs = myco.diffs
	}
}