WIP: empty tests

.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:

.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

.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

.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:

.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:

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.