From fb91a02460b22501cc1c57dc381a486a29b01fbd Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Thu, 27 Jan 2022 12:01:28 +0100
Subject: [PATCH] update healthchecker
---
hmftools.wdl | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/hmftools.wdl b/hmftools.wdl
index 0b4ba6d..76620e3 100644
--- a/hmftools.wdl
+++ b/hmftools.wdl
@@ -408,13 +408,16 @@ task HealthChecker {
-tum_flagstat_file ~{tumorFlagstats} \
-tum_wgs_metrics_file ~{tumorMetrics} \
-purple_dir ~{sub(purpleOutput[0], basename(purpleOutput[0]), "")} \
- -output_dir ~{outputDir}
+ -output_dir ~{outputDir}
+ test -e '~{outputDir}/~{tumorName}.HealthCheckSucceeded' && echo 'true' > '~{outputDir}/succeeded'
+ test -e '~{outputDir}/~{tumorName}.HealthCheckFailed' && echo 'false' > '~{outputDir}/succeeded'
}
-
output {
- File? healthCheckSucceeded = "~{outputDir}/~{tumorName}.HealthCheckSucceeded"
- File? healthCheckFailed = "~{outputDir}/~{tumorName}.HealthCheckFailed"
+ Boolean succeeded = read_boolean("result")
+ File outputFile = if succeeded
+ then "~{outputDir}/~{tumorName}.HealthCheckSucceeded"
+ else "~{outputDir}/~{tumorName}.HealthCheckFailed"
}
runtime {
--
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