stjudecloud · adthrasher · May 18, 2026
diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl
@@ -67,6 +67,7 @@ struct FlagFilter {
     String exclude_if_all  # samtools -G
 }
 
+#@ except: EmptyOutputs
 task validate_string_is_12bit_int {
     meta {
         description: "Validates that a string is a octal, decimal, or hexadecimal number and less than 2^12."

diff --git a/data_structures/read_group.wdl b/data_structures/read_group.wdl
@@ -143,6 +143,7 @@ task get_read_groups {
     }
 }
 
+#@ except: EmptyOutputs
 task validate_read_group {
     meta {
         description: "Validate a `ReadGroup` struct's fields are defined and well-formed"

diff --git a/tools/fq.wdl b/tools/fq.wdl
@@ -1,6 +1,7 @@
 ## [Homepage](https://github.com/stjude-rust-labs/fq)
 version 1.1
 
+#@ except: EmptyOutputs
 task fqlint {
     meta {
         description: "Performs quality control on the input FASTQs to ensure proper formatting"

diff --git a/tools/samtools.wdl b/tools/samtools.wdl
@@ -3,6 +3,7 @@ version 1.1
 
 import "../data_structures/flag_filter.wdl"
 
+#@ except: EmptyOutputs
 task quickcheck {
     meta {
         description: "Runs Samtools quickcheck on the input BAM file."

diff --git a/tools/util.wdl b/tools/util.wdl
@@ -132,6 +132,7 @@ task calc_feature_lengths {
     }
 }
 
+#@ except: EmptyOutputs
 task compression_integrity {
     meta {
         description: "Checks the compression integrity of a bgzipped file"
@@ -358,6 +359,7 @@ task global_phred_scores {
     }
 }
 
+#@ except: EmptyOutputs
 task check_fastq_and_rg_concordance {
     meta {
         description: "Validates FASTQs and read group records are concordant"

diff --git a/workflows/dnaseq/dnaseq-standard.wdl b/workflows/dnaseq/dnaseq-standard.wdl
@@ -133,6 +133,7 @@ workflow dnaseq_standard_experimental {
     }
 }
 
+#@ except: EmptyOutputs
 task parse_input {
     meta {
         description: "Parses and validates the `dnaseq_standard` workflow's provided inputs"

diff --git a/workflows/rnaseq/rnaseq-standard.wdl b/workflows/rnaseq/rnaseq-standard.wdl
@@ -141,6 +141,7 @@ workflow rnaseq_standard {
     }
 }
 
+#@ except: EmptyOutputs
 task parse_input {
     meta {
         description: "Parses and validates the `rnaseq_standard[_fastq]` workflows' provided inputs"
-Original file line number
+Diff line change
@@ Expand Up / @@ -143,6 +143,7 @@ task get_read_groups { @@
         }
     }
+    #@ except: EmptyOutputs
     task validate_read_group {
         meta {
             description: "Validate a `ReadGroup` struct's fields are defined and well-formed"
@@ Expand Down @@