/
wf_pangolin_update.wdl
59 lines (57 loc) · 2.07 KB
/
wf_pangolin_update.wdl
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version 1.0
import "../tasks/task_taxonID.wdl" as taxon_ID
import "../tasks/task_versioning.wdl" as versioning
workflow pangolin_update {
input {
String samplename
File assembly
String current_lineage
String current_pangolin_docker
String current_pangolin_assignment_version
String current_pangolin_versions
String updated_pangolin_docker
String? timezone
File? lineage_log
}
call taxon_ID.pangolin4 {
input:
samplename = samplename,
fasta = assembly,
docker = updated_pangolin_docker
}
call taxon_ID.pangolin_update_log {
input:
samplename = samplename,
current_lineage = current_lineage,
current_pangolin_docker = current_pangolin_docker,
current_pangolin_assignment_version = current_pangolin_assignment_version,
current_pangolin_versions = current_pangolin_versions,
updated_lineage = pangolin4.pangolin_lineage,
updated_pangolin_docker = pangolin4.pangolin_docker,
updated_pangolin_assignment_version = pangolin4.pangolin_assignment_version,
updated_pangolin_versions = pangolin4.pangolin_versions,
timezone = timezone,
lineage_log = lineage_log
}
call versioning.version_capture{
input:
timezone = timezone
}
output {
# Version Capture
String pangolin_update_version = version_capture.phvg_version
String pangolin_update_analysis_date = version_capture.date
# Pangolin Assignments
String pango_lineage = pangolin4.pangolin_lineage
String pangolin_conflicts = pangolin4.pangolin_conflicts
String pangolin_notes = pangolin4.pangolin_notes
String pangolin_assignment_version = pangolin4.pangolin_assignment_version
String pangolin_versions = pangolin4.pangolin_versions
File pango_lineage_report = pangolin4.pango_lineage_report
String pangolin_docker = pangolin4.pangolin_docker
String pango_lineage_expanded = pangolin4.pangolin_lineage_expanded
# Update Log
String pangolin_updates = pangolin_update_log.pangolin_updates
File pango_lineage_log = pangolin_update_log.pango_lineage_log
}
}