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wes_upstream_gatk4.wdl
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wes_upstream_gatk4.wdl
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import "wes_upstream_1SampleFastqs_gatk4.wdl" as sample_wf
workflow wes_upstream
{
#RESOURCES SECTION
File dbSNP_vcf
File dbSNP_vcf_idx
String known_indels_sites_VCF
String known_indels_sites_idx
String ref_fasta
File ref_dict
File scattered_calling_intervals_list
#INPUT SECTION
Map[String, Pair[File, File]] input_fastqs #Map that links a sample to the pair of FASTQ files
String tools #Path to the directory that contains all needed tools and scripts
String base_name #Base name that will be used in every output file.
String res_dir #Path to the directory that will contain the results of the upstream run
Int bwa_threads
Int samtools_threads
#For every sample call the upstream sub-workflow
scatter(key_value in input_fastqs)
{
String key_sampleName = key_value.left
Pair[File, File] value_fastqs = key_value.right
call sample_wf.wes {
input:
sampleName = key_sampleName,
fastq1 = value_fastqs.left,
fastq2 = value_fastqs.right,
bwa_threads = bwa_threads,
samtools_threads = samtools_threads,
tools = tools,
base_name = base_name,
res_dir = res_dir,
dbSNP_vcf = dbSNP_vcf,
dbSNP_vcf_idx = dbSNP_vcf_idx,
known_indels_sites_VCF = known_indels_sites_VCF,
known_indels_sites_idx = known_indels_sites_idx,
ref_fasta = ref_fasta,
ref_dict = ref_dict,
scattered_calling_intervals_list = scattered_calling_intervals_list
}
}
}