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cnest_part0.wdl
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cnest_part0.wdl
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version 1.0
workflow CnestWorkflow {
input {
String project
File bedgz
}
call step0 {
input:
bedgz = bedgz
}
call step1 {
input:
bed = step0.ch_bed,
project = project
}
output{
File out_ch_index_tab = step1.ch_index_tab
File out_ch_index = step1.ch_index
File out_ch_index_bed = step1.ch_index_bed
}
}
task step0 {
input {
File bedgz
}
String bed_name = basename(bedgz, ".gz")
command {
gzip -cd ~{bedgz} > ~{bed_name}
}
output{
File ch_bed = "~{bed_name}"
}
runtime{
docker: "tomas81/cnest:dev"
}
}
task step1 {
input {
File bed
String project
}
command {
cnest.py step1 --project ~{project} --bed ~{bed}
}
output{
File ch_index_tab = "~{project}/index_tab.txt"
File ch_index = "~{project}/index.txt"
File ch_index_bed = "~{project}/index.bed"
}
runtime{
docker: "tomas81/cnest:dev"
}
}