diff --git a/.github/workflows/miniwdl-check.yaml b/.github/workflows/miniwdl-check.yaml
index 14fa817bc..479ffc234 100644
--- a/.github/workflows/miniwdl-check.yaml
+++ b/.github/workflows/miniwdl-check.yaml
@@ -6,7 +6,7 @@ jobs:
   miniwdl_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python
       uses: actions/setup-python@v1
       with:
diff --git a/.github/workflows/pull-check.yaml b/.github/workflows/pull-check.yaml
index 6e935017b..b8850b3c6 100644
--- a/.github/workflows/pull-check.yaml
+++ b/.github/workflows/pull-check.yaml
@@ -10,7 +10,7 @@ jobs:
   import_syntax_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Check import syntax
       run: |
         EXITCODE=0
@@ -41,7 +41,7 @@ jobs:
   docker_pull_check:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Ensure current SemVer'd docker images are being pulled
       run: |
         EXITCODE=0
diff --git a/.github/workflows/sprocket-check.yaml b/.github/workflows/sprocket-check.yaml
index a2cc9ca39..5338d9497 100644
--- a/.github/workflows/sprocket-check.yaml
+++ b/.github/workflows/sprocket-check.yaml
@@ -6,6 +6,6 @@ jobs:
     sprocket_check:
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v4
         - name: Run sprocket
           uses: stjude-rust-labs/sprocket-action@main
diff --git a/.github/workflows/sprocket-lint.yaml b/.github/workflows/sprocket-lint.yaml
index 2c743964b..0b7f286e5 100644
--- a/.github/workflows/sprocket-lint.yaml
+++ b/.github/workflows/sprocket-lint.yaml
@@ -6,7 +6,7 @@ jobs:
     sprocket_lint:
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v4
         - name: Run sprocket
           uses: stjude-rust-labs/sprocket-action@main
           with:
diff --git a/.github/workflows/validate-inputs.yaml b/.github/workflows/validate-inputs.yaml
index 80b42a84f..e645e5636 100644
--- a/.github/workflows/validate-inputs.yaml
+++ b/.github/workflows/validate-inputs.yaml
@@ -6,7 +6,7 @@ jobs:
     validate_inputs:
         runs-on: ubuntu-latest
         steps:
-        - uses: actions/checkout@v2
+        - uses: actions/checkout@v4
         - name: Validate Reference Inputs
           uses: stjude-rust-labs/sprocket-action@main
           with:
diff --git a/tests/input/GRCh38.chrY_chrM.fa.gz b/tests/input/GRCh38.chrY_chrM.fa.gz
new file mode 100644
index 000000000..7c87e51af
--- /dev/null
+++ b/tests/input/GRCh38.chrY_chrM.fa.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c24bb220de848ea993a67841ca9de65c3c6bb2783a2abbb03cfb75a09a429af4
+size 7060411
diff --git a/tests/input/README.md b/tests/input/README.md
index d03cdd5da..d4bbf554a 100644
--- a/tests/input/README.md
+++ b/tests/input/README.md
@@ -40,6 +40,22 @@ Intervals for `chr1` (and one interval from `chr19`) derived from `wgs_calling_r
 
 Combined beta values from `minfi` for two patient samples.
 
+## empty.chrY_chrM.Aligned.out.bam
+
+The result of passing `empty.r[1,2].fq.gz` into STAR alignment.
+
+## empty.chrY_chrM.bwa_aln.SE.bam
+
+The result of passing `empty.r1.fq.gz` into BWA aln Single-End alignment.
+
+## empty.r1.fq.gz
+
+A gzipped FASTQ file without any reads inside.
+
+## empty.r2.fq.gz
+
+A gzipped FASTQ file without any reads inside.
+
 ## filtered_beta.csv
 
 Beta values from `minfi` filtered to the top 10K most differentially methylated probes.
@@ -96,6 +112,10 @@ FASTA format GRCh38 reference containing `chrY` and `chrM` only
 
 FASTA index for GRCh38 reference containing `chrY` and `chrM` only
 
+## GRCh38.chrY_chrM.fa.gz
+
+Gzipped `GRCh38.chrY_chrM.fa`
+
 ## Homo_sapiens_assembly38.dbsnp138.top5000.vcf
 
 First 5000 records for hg38 from dbsnp version 138.
diff --git a/tests/input/empty.chrY_chrM.Aligned.out.bam b/tests/input/empty.chrY_chrM.Aligned.out.bam
new file mode 100644
index 000000000..9d96f9b73
--- /dev/null
+++ b/tests/input/empty.chrY_chrM.Aligned.out.bam
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:e9b67b09b4957e3b0496611bf2cdba1f58a91d27e7c07c015081f624ef831079
+size 2062
diff --git a/tests/input/empty.chrY_chrM.bwa_aln.SE.bam b/tests/input/empty.chrY_chrM.bwa_aln.SE.bam
new file mode 100644
index 000000000..dfc0acc66
--- /dev/null
+++ b/tests/input/empty.chrY_chrM.bwa_aln.SE.bam
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b98c4e371b1a725a5a7d785ee52c063454e540307ee1f53daca880d9378c08b0
+size 281
diff --git a/tests/input/empty.r1.fq.gz b/tests/input/empty.r1.fq.gz
new file mode 100644
index 000000000..9badddd05
--- /dev/null
+++ b/tests/input/empty.r1.fq.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ac73670af3abed54ac6fb4695131f4099be9fbe39d6076c5d0264a6bbdae9d83
+size 20
diff --git a/tests/input/empty.r2.fq.gz b/tests/input/empty.r2.fq.gz
new file mode 100644
index 000000000..9badddd05
--- /dev/null
+++ b/tests/input/empty.r2.fq.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:ac73670af3abed54ac6fb4695131f4099be9fbe39d6076c5d0264a6bbdae9d83
+size 20