From 26bfacb6206024c06714a0fb3f837de4a782ae26 Mon Sep 17 00:00:00 2001
From: Matthew Angel <matthew.g.angel@gmail.com>
Date: Wed, 20 May 2026 14:42:21 -0400
Subject: [PATCH] add testing

---
 modules/find_switchback_reads.nf |  7 +++++++
 tests/main.nf.test.snap          | 12 +++++++-----
 2 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/modules/find_switchback_reads.nf b/modules/find_switchback_reads.nf
index cd3f27e..248b05e 100644
--- a/modules/find_switchback_reads.nf
+++ b/modules/find_switchback_reads.nf
@@ -21,4 +21,11 @@ process find_switchback_reads {
         --metrics ${library}.switchbacks \\
         --ref ${genome_fa}
     """
+
+    stub:
+    """
+    touch ${library}.switchbacks.bam
+    printf 'sample\tlibrary\ttemplates\taligned_templates\tswitchback_templates\tfraction_switchbacks\tread_based_switchbacks\tmean_length\tmean_offset\ttandem_based_switchbacks\tmean_gap\n' > ${library}.switchbacks.summary.txt
+    printf '${library}\t${library}\t0\t0\t0\t0.0\t0\t0.0\t0.0\t0\t0.0\n' >> ${library}.switchbacks.summary.txt
+    """
 }
diff --git a/tests/main.nf.test.snap b/tests/main.nf.test.snap
index 24a5025..d757b75 100644
--- a/tests/main.nf.test.snap
+++ b/tests/main.nf.test.snap
@@ -3,8 +3,8 @@
         "content": [
             {
                 "tasksFailed": 0,
-                "tasksCount": 57,
-                "tasksSucceeded": 57
+                "tasksCount": 59,
+                "tasksSucceeded": 59
             },
             [
                 "bwameth_file_1",
@@ -356,7 +356,8 @@
                     "--fastqc emseq-test1.md_fastqc.zip ",
                     "--nonconverted_read_counts emseq-test1.nonconverted_counts.for_agg.tsv ",
                     "--tasmanian emseq-test1.tasmanian.csv ",
-                    "--combined_mbias_records emseq-test1.combined_mbias.tsv",
+                    "--combined_mbias_records emseq-test1.combined_mbias.tsv ",
+                    "--fgbio_switchbacks emseq-test1.switchbacks.summary.txt",
                     "--workflow EM-seq"
                 ]
             ]
@@ -371,8 +372,8 @@
         "content": [
             {
                 "tasksFailed": 0,
-                "tasksCount": 49,
-                "tasksSucceeded": 49
+                "tasksCount": 51,
+                "tasksSucceeded": 51
             },
             [
                 "bwameth_file_1",
@@ -687,6 +688,7 @@
                     "--nonconverted_read_counts emseq-test1.nonconverted_counts.for_agg.tsv ",
                     "--tasmanian emseq-test1.tasmanian.csv ",
                     "--combined_mbias_records emseq-test1.combined_mbias.tsv ",
+                    "--fgbio_switchbacks emseq-test1.switchbacks.summary.txt ",
                     "--insert emseq-test1.insertsize_metrics",
                     "--workflow EM-seq"
                 ]