update regression tests with no default discarded and demultiplexing …

…--out options
MikkelSchubert · Jul 28, 2024 · 078a5b6 · 078a5b6
1 parent bec1e96
commit 078a5b6
Show file tree

Hide file tree

Showing 189 changed files with 763 additions and 95 deletions.
diff --git a/scripts/regression_test_runner.py b/scripts/regression_test_runner.py
@@ -252,13 +252,20 @@ def classname(v: object) -> str:
 
 ################################################################################
 
+
+def _is_str_list(value: object) -> bool:
+    return isinstance(value, list) and all(
+        isinstance(v, str) for v in cast(List[object], value)
+    )
+
+
 # Wildcards with (limited) type checking
 JSON_WILDCARDS: dict[str, Callable[[object], bool]] = {
     "...": lambda _: True,
     "...str": lambda it: isinstance(it, str),
     "...float": lambda it: isinstance(it, float) and not math.isnan(it),
-    "...[str]": lambda it: isinstance(it, list)
-    and all(isinstance(v, str) for v in cast(List[object], it)),
+    "...[str]": _is_str_list,
+    "...[str] | None": lambda it: it is None or _is_str_list(it),
 }
 
 # JSON path elements that do not require quoting
@@ -540,7 +547,7 @@ def _mask_filenames(data: JSON) -> JSON:
                 data = dict(data)
                 for key, value in data.items():
                     if key == "filenames":
-                        data[key] = "...[str]"
+                        data[key] = "...[str] | None"
                     else:
                         new_value = _mask_filenames(value)
                         if new_value is not value:

diff --git a/tests/regression/adapter_trimming/excl_adapter/pe/non_overlapping/test.json b/tests/regression/adapter_trimming/excl_adapter/pe/non_overlapping/test.json
@@ -11,7 +11,6 @@
       "input_2.fastq"
     ],
     "output": [
-      "your_output.discarded.fastq",
       "your_output.r1.fastq",
       "your_output.r2.fastq",
       "your_output.singleton.fastq"

diff --git a/tests/regression/adapter_trimming/excl_adapter/pe/non_overlapping/your_output.json b/tests/regression/adapter_trimming/excl_adapter/pe/non_overlapping/your_output.json
@@ -173,7 +173,7 @@
       "gc_content": null
     },
     "discarded": {
-      "filenames": ["your_output.discarded.fastq"],
+      "filenames": null,
       "input_reads": 0,
       "output_reads": 0,
       "reads_sampled": 0,

diff --git a/tests/regression/adapter_trimming/excl_adapter/pe/overlapping/test.json b/tests/regression/adapter_trimming/excl_adapter/pe/overlapping/test.json
@@ -11,7 +11,6 @@
       "input_2.fastq"
     ],
     "output": [
-      "your_output.discarded.fastq",
       "your_output.r1.fastq",
       "your_output.r2.fastq",
       "your_output.singleton.fastq"

diff --git a/tests/regression/adapter_trimming/excl_adapter/pe/overlapping/your_output.json b/tests/regression/adapter_trimming/excl_adapter/pe/overlapping/your_output.json
@@ -173,7 +173,7 @@
       "gc_content": null
     },
     "discarded": {
-      "filenames": ["your_output.discarded.fastq"],
+      "filenames": null,
       "input_reads": 0,
       "output_reads": 0,
       "reads_sampled": 0,

diff --git a/tests/regression/adapter_trimming/excl_adapter/se/test.json b/tests/regression/adapter_trimming/excl_adapter/se/test.json
@@ -8,7 +8,6 @@
       "input_1.fastq"
     ],
     "output": [
-      "your_output.discarded.fastq",
       "your_output.r1.fastq"
     ],
     "json": [

diff --git a/tests/regression/adapter_trimming/excl_adapter/se/your_output.json b/tests/regression/adapter_trimming/excl_adapter/se/your_output.json
@@ -118,7 +118,7 @@
     "unidentified_2": null,
     "singleton": null,
     "discarded": {
-      "filenames": ["your_output.discarded.fastq"],
+      "filenames": null,
       "input_reads": 0,
       "output_reads": 0,
       "reads_sampled": 0,

diff --git a/tests/regression/adapter_trimming/incl_adapter/pe/test_defaults.json b/tests/regression/adapter_trimming/incl_adapter/pe/test_defaults.json
@@ -13,7 +13,6 @@
       "input_2.fastq"
     ],
     "output": [
-      "your_output.discarded.fastq",
       "your_output.r1.fastq",
       "your_output.r2.fastq",
       "your_output.singleton.fastq"

diff --git a/tests/regression/adapter_trimming/incl_adapter/pe/your_output.json b/tests/regression/adapter_trimming/incl_adapter/pe/your_output.json
@@ -173,7 +173,7 @@
       "gc_content": null
     },
     "discarded": {
-      "filenames": ["your_output.discarded.fastq"],
+      "filenames": null,
       "input_reads": 0,
       "output_reads": 0,
       "reads_sampled": 0,

diff --git a/tests/regression/adapter_trimming/incl_adapter/se/test_defaults.json b/tests/regression/adapter_trimming/incl_adapter/se/test_defaults.json
@@ -10,7 +10,6 @@
       "input_1.fastq"
     ],
     "output": [
-      "your_output.discarded.fastq",
       "your_output.r1.fastq"
     ],
     "json": [

diff --git a/tests/regression/adapter_trimming/incl_adapter/se/your_output.discarded.fastq b/tests/regression/adapter_trimming/incl_adapter/se/your_output.discarded.fastq
diff --git a/tests/regression/adapter_trimming/incl_adapter/se/your_output.json b/tests/regression/adapter_trimming/incl_adapter/se/your_output.json
@@ -118,7 +118,7 @@
     "unidentified_2": null,
     "singleton": null,
     "discarded": {
-      "filenames": ["your_output.discarded.fastq"],
+      "filenames": null,
       "input_reads": 0,
       "output_reads": 0,
       "reads_sampled": 0,

diff --git a/tests/regression/adapter_trimming/only_adapter/pe/test.json b/tests/regression/adapter_trimming/only_adapter/pe/test.json
@@ -1,7 +1,9 @@
 {
   "arguments": [
     "--basename",
-    "your_output"
+    "your_output",
+    "--out-discarded",
+    "your_output.discarded.fastq"
   ],
   "files": {
     "input_1": [

diff --git a/tests/regression/adapter_trimming/only_adapter/se/test.json b/tests/regression/adapter_trimming/only_adapter/se/test.json
@@ -1,7 +1,9 @@
 {
   "arguments": [
     "--basename",
-    "your_output"
+    "your_output",
+    "--out-discarded",
+    "your_output.discarded.fastq"
   ],
   "files": {
     "input_1": [

diff --git a/tests/regression/demultiplexing/common/basenames/barcodes.txt b/tests/regression/demultiplexing/common/basenames/barcodes.txt
@@ -0,0 +1,2 @@
+sample_1	TGAGTCAT	GTTAGTGG
+sample_2	GCAGAGAT	CCTAGGGT
diff --git a/tests/regression/demultiplexing/common/basenames/basename_1.json b/tests/regression/demultiplexing/common/basenames/basename_1.json
diff --git a/...n_overlapping/your_output.discarded.fastq → ...asenames/basename_1.unidentified.r1.fastq b/...n_overlapping/your_output.discarded.fastq → ...asenames/basename_1.unidentified.r1.fastq
diff --git a/...e/overlapping/your_output.discarded.fastq → ...asenames/basename_1.unidentified.r2.fastq b/...e/overlapping/your_output.discarded.fastq → ...asenames/basename_1.unidentified.r2.fastq
diff --git a/tests/regression/demultiplexing/common/basenames/basename_2.sample_1.discarded.fastq b/tests/regression/demultiplexing/common/basenames/basename_2.sample_1.discarded.fastq
@@ -0,0 +1,4 @@
+@read_s1_000
+
++
+
diff --git a/tests/regression/demultiplexing/common/basenames/basename_2.sample_2.discarded.fastq b/tests/regression/demultiplexing/common/basenames/basename_2.sample_2.discarded.fastq
@@ -0,0 +1,4 @@
+@read_s2_000
+
++
+
diff --git a/tests/regression/demultiplexing/common/basenames/basename_3.sample_1.merged.fastq b/tests/regression/demultiplexing/common/basenames/basename_3.sample_1.merged.fastq
@@ -0,0 +1,8 @@
+@read_s1_075
+GCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACC
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG
+@read_s1_150
+AGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTTGAAAGTACCAAAGGAGTATCACCAGTACGTGAGAAGTGAGCGGTTGCTATAACCACAT
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;<<<====>>>?????@@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG
diff --git a/tests/regression/demultiplexing/common/basenames/basename_3.sample_2.merged.fastq b/tests/regression/demultiplexing/common/basenames/basename_3.sample_2.merged.fastq
@@ -0,0 +1,8 @@
+@read_s2_075
+CCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTAC
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG
+@read_s2_150
+TAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGAGCACAATCAGATAATAATATGCTGATCGTCAACAATTGGGTACTGCCGAATCGAGAGG
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;<<<====>>>?????@@@@AAAAAABBBBBBCCCCCCCDDDDDDDEEEEEEEEEFFFFFFFFFGGGGGGGGGGG
diff --git a/...cl_adapter/se/your_output.discarded.fastq → ...names/basename_4.sample_1.singleton.fastq b/...cl_adapter/se/your_output.discarded.fastq → ...names/basename_4.sample_1.singleton.fastq
diff --git a/...cl_adapter/pe/your_output.discarded.fastq → ...names/basename_4.sample_2.singleton.fastq b/...cl_adapter/pe/your_output.discarded.fastq → ...names/basename_4.sample_2.singleton.fastq
diff --git a/tests/regression/demultiplexing/common/basenames/basename_5.sample_1.r1.fastq b/tests/regression/demultiplexing/common/basenames/basename_5.sample_1.r1.fastq
@@ -0,0 +1,4 @@
+@read_s1_200/1
+ACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
diff --git a/tests/regression/demultiplexing/common/basenames/basename_5.sample_2.r1.fastq b/tests/regression/demultiplexing/common/basenames/basename_5.sample_2.r1.fastq
@@ -0,0 +1,4 @@
+@read_s2_200/1
+GCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
diff --git a/tests/regression/demultiplexing/common/basenames/basename_6.sample_1.r2.fastq b/tests/regression/demultiplexing/common/basenames/basename_6.sample_1.r2.fastq
@@ -0,0 +1,4 @@
+@read_s1_200/2
+GATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
diff --git a/tests/regression/demultiplexing/common/basenames/basename_6.sample_2.r2.fastq b/tests/regression/demultiplexing/common/basenames/basename_6.sample_2.r2.fastq
@@ -0,0 +1,4 @@
+@read_s2_200/2
+TTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA
++
+GGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
diff --git a/tests/regression/demultiplexing/common/basenames/input_1.fastq b/tests/regression/demultiplexing/common/basenames/input_1.fastq
@@ -0,0 +1,32 @@
+@read_s2_000/1
+GCAGAGATACCCTAGGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s2_075/1
+GCAGAGATCCTACAAAAGTTAAGTGCGCGTTTGGGCATCGTCCCGACGACTTCCGCTGAGTTGACTTAATGGCTTGTCGGTACACCCTAGGAGATCGGAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_000/1
+TGAGTCATCCACTAACAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAACCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_075/1
+TGAGTCATGCACAGTTACACTGCCGTTTGTCTGTCCATGTAATTGTCTAATCACTTTAGAATACGGCTCCTGATATCATCACCCCACTAACAGATCGGAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_200/1
+TGAGTCATACATCCAAGTCGGGCAACCTCTCACATTACTTAGGCCAGGCACTTGCACATCGAAGCAAAGGAGAGATAATTGCCGTATCCTCTGTGCACGT
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s2_200/1
+GCAGAGATGCCCATAAAATATTGCTCGCAACGGTATGCTAGACCCAGGACATCCGCTTTATCCGTGGTGATAGCAACTGGAGGCATCTAACGTTCACACG
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_150/1
+TGAGTCATAGAATGAGCGGGGTCGACTCGTAACGATCTCTGCAGGGCGATGGTCTACATAGGCCCCACATCCAGATTATCTCGTAAAAGGAAAAACGGTT
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s2_150/1
+GCAGAGATTAGCCCCCGGGGTGTGGGGTTTTGCTTCCGCCACAAAAATGGTGCGCTAAATGACCATTGCGTACACTCCAACGCGAAATGTAGGGCGCCGA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
diff --git a/tests/regression/demultiplexing/common/basenames/input_2.fastq b/tests/regression/demultiplexing/common/basenames/input_2.fastq
@@ -0,0 +1,32 @@
+@read_s2_000/2
+CCTAGGGTATCTCTGCAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s2_075/2
+CCTAGGGTGTACCGACAAGCCATTAAGTCAACTCAGCGGAAGTCGTCGGGACGATGCCCAAACGCGCACTTAACTTTTGTAGGATCTCTGCAGATCGGAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_000/2
+GTTAGTGGATGACTCAAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_075/2
+GTTAGTGGGGTGATGATATCAGGAGCCGTATTCTAAAGTGATTAGACAATTACATGGACAGACAAACGGCAGTGTAACTGTGCATGACTCAAGATCGGAA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_200/2
+GTTAGTGGGATAATACGCTCTAGAGAAAAAGAGTGATAAGTGAATAACCGGGCTATAGTGACAAAGAATTCCGCGTTACTAAATCACCCAACCCACCTTC
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s2_200/2
+CCTAGGGTTTACTTTTGATTCAACACCGACTTGGTCCCGCCTCCACGTGCAACACCCCCTTTTAATAGCAACGCGCTCACCGAGGCTCCTCCCATCCACA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s1_150/2
+GTTAGTGGATGTGGTTATAGCAACCGCTCACTTCTCACGTACTGGTGATACTCCTTTGGTACTTTCAACCGTTTTTCCTTTTACGAGATAATCTGGATGT
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
+@read_s2_150/2
+CCTAGGGTCCTCTCGATTCGGCAGTACCCAATTGTTGACGATCAGCATATTATTATCTGATTGTGCTCGGCGCCCTACATTTCGCGTTGGAGTGTACGCA
++
+HHHHHHHHGGGGGGGGGGGFFFFFFFFFEEEEEEEEEDDDDDDDCCCCCCCBBBBBBAAAAAA@@@@?????>>>====<<<;;:::9988766543210
diff --git a/tests/regression/demultiplexing/common/basenames/test.json b/tests/regression/demultiplexing/common/basenames/test.json
@@ -0,0 +1,52 @@
+{
+  "description": "Demultiplexing, trimming, and merging of PE reads with custom basenames",
+  "exhaustive": true,
+  "arguments": [
+    "--basename",
+    "basename_1",
+    "--out-discarded",
+    "basename_2",
+    "--out-merged",
+    "basename_3",
+    "--out-singleton",
+    "basename_4",
+    "--out-file1",
+    "basename_5",
+    "--out-file2",
+    "basename_6",
+    "--barcode-list",
+    "barcodes.txt",
+    "--merge"
+  ],
+  "files": {
+    "input_1": [
+      "input_1.fastq"
+    ],
+    "input_2": [
+      "input_2.fastq"
+    ],
+    "barcodes": [
+      "barcodes.txt"
+    ],
+    "output": [
+      "basename_1.unidentified.r1.fastq",
+      "basename_1.unidentified.r2.fastq",
+      "basename_2.sample_1.discarded.fastq",
+      "basename_2.sample_2.discarded.fastq",
+      "basename_3.sample_1.merged.fastq",
+      "basename_3.sample_2.merged.fastq",
+      "basename_4.sample_1.singleton.fastq",
+      "basename_4.sample_2.singleton.fastq",
+      "basename_5.sample_1.r1.fastq",
+      "basename_5.sample_2.r1.fastq",
+      "basename_6.sample_1.r2.fastq",
+      "basename_6.sample_2.r2.fastq"
+    ],
+    "json": [
+      "basename_1.json"
+    ],
+    "html": [
+      "basename_1.html"
+    ]
+  }
+}
diff --git a/tests/regression/demultiplexing/common/interleaved/test.json b/tests/regression/demultiplexing/common/interleaved/test.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--interleaved-output"

diff --git a/tests/regression/demultiplexing/common/merge/test.json b/tests/regression/demultiplexing/common/merge/test.json
@@ -4,6 +4,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--merge"

diff --git a/tests/regression/demultiplexing/double_indexed/pe/test_1_thread.json b/tests/regression/demultiplexing/double_indexed/pe/test_1_thread.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--threads",

diff --git a/tests/regression/demultiplexing/double_indexed/pe/test_2_threads.json b/tests/regression/demultiplexing/double_indexed/pe/test_2_threads.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--threads",

diff --git a/tests/regression/demultiplexing/double_indexed/pe/test_3_threads.json b/tests/regression/demultiplexing/double_indexed/pe/test_3_threads.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--threads",

diff --git a/tests/regression/demultiplexing/double_indexed/pe/test_defaults.json b/tests/regression/demultiplexing/double_indexed/pe/test_defaults.json
@@ -4,6 +4,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt"
   ],

diff --git a/tests/regression/demultiplexing/double_indexed/se/test_1_thread.json b/tests/regression/demultiplexing/double_indexed/se/test_1_thread.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--threads",

diff --git a/tests/regression/demultiplexing/double_indexed/se/test_2_threads.json b/tests/regression/demultiplexing/double_indexed/se/test_2_threads.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--threads",

diff --git a/tests/regression/demultiplexing/double_indexed/se/test_3_threads.json b/tests/regression/demultiplexing/double_indexed/se/test_3_threads.json
@@ -3,6 +3,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt",
     "--threads",

diff --git a/tests/regression/demultiplexing/double_indexed/se/test_defaults.json b/tests/regression/demultiplexing/double_indexed/se/test_defaults.json
@@ -4,6 +4,8 @@
   "arguments": [
     "--basename",
     "your_output",
+    "--out-discarded",
+    "your_output",
     "--barcode-list",
     "barcodes.txt"
   ],
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample_1 TGAGTCAT GTTAGTGG
		sample_2 GCAGAGAT CCTAGGGT