From 35a5ecaaade025b04e8bcb30efc796a722239c23 Mon Sep 17 00:00:00 2001
From: Andrew Thrasher <adthrasher@gmail.com>
Date: Mon, 18 May 2026 11:39:45 -0400
Subject: [PATCH] chore: exceptions for tasks with no outputs

---
 data_structures/flag_filter.wdl      | 1 +
 data_structures/read_group.wdl       | 1 +
 tools/fq.wdl                         | 1 +
 tools/samtools.wdl                   | 1 +
 tools/util.wdl                       | 2 ++
 workflows/dnaseq/dnaseq-standard.wdl | 1 +
 workflows/rnaseq/rnaseq-standard.wdl | 1 +
 7 files changed, 8 insertions(+)

diff --git a/data_structures/flag_filter.wdl b/data_structures/flag_filter.wdl
index 3e23f724a..dcbf73e8f 100644
--- 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
index 94632b4c6..bde09af24 100644
--- 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
index bffb332be..e2d5c566a 100755
--- 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
index ace383ece..d0ad37742 100755
--- 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
index 319d72ed9..2a82680c8 100644
--- 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
index f0a481509..faa9be835 100644
--- 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
index ae5c53641..d100a9af7 100755
--- 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"