From f6785dafb84714f2b303344219e13543ed3d0947 Mon Sep 17 00:00:00 2001
From: Julian Libiseller-Egger <julian.libiseller-egger@nanoporetech.com>
Date: Mon, 10 Jul 2023 15:11:33 +0000
Subject: [PATCH] fix bug making mosdepth fail when length of the reference was
 smaller than --number_depth_windows [CW-2372]

---
 CHANGELOG.md              |  4 ++++
 modules/local/pipeline.nf | 12 ++++++++----
 nextflow.config           |  2 +-
 3 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 74703c2..62d6090 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.2.2]
+### Fixed
+- Bug where the `mosdepth` process would fail if the length of a reference sequence was smaller than the number of depth windows requested.
+
 ## [v0.2.1]
 ### Changed
 - GitHub issue templates
diff --git a/modules/local/pipeline.nf b/modules/local/pipeline.nf
index f530cfd..7f38709 100644
--- a/modules/local/pipeline.nf
+++ b/modules/local/pipeline.nf
@@ -37,12 +37,16 @@ process mosdepth {
     script:
     int mosdepth_extra_threads = task.cpus - 1
     """
-    # get window length for reference
+    # get the length of the reference
     ref_length=\$(samtools idxstats input.bam | awk '\$1 == "$ref_id" {print \$2}')
-    window_length=\$(expr \$ref_length / $n_windows)
 
-    # if the reference is very short, `window_length` might be `0` --> set to `1`
-    [ "\$window_length" -eq "0" ] && window_length=1
+    # calculate the corresponding window length (check `ref_length` first because
+    # `expr a / b` returns non-zero exit code when `a < b`)
+    if [ "\$ref_length" -lt "$n_windows" ]; then
+        window_length=1
+    else
+        window_length=\$(expr \$ref_length / $n_windows)
+    fi
 
     # get the depths (we could add `-x`, but it loses a lot of detail from the depth
     # curves)
diff --git a/nextflow.config b/nextflow.config
index d9b2aa7..d95620a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -65,7 +65,7 @@ manifest {
     description     = 'Amplicon workflow'
     mainScript      = 'main.nf'
     nextflowVersion = '>=22.10.8'
-    version         = 'v0.2.1'
+    version         = 'v0.2.2'
 }
 
 epi2melabs {