Merge branch 'CW-3367' into 'dev'

fix depth plots [CW-3367]

Closes CW-3367

See merge request epi2melabs/workflows/wf-alignment!123

CHANGELOG.md

@@ -4,7 +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).
 
-## [unreleased]
+## [v1.0.3]
+### Fixed
+- Fix regression in depth plots that concatenated the curves of the different samples, rather than displaying them as a multi-line plot
+
 ### Changed
 - BAM tags from uBAM inputs are now carried over to the resulting BAM files.
 

bin/workflow_glue/report_utils/sections.py

@@ -462,8 +462,11 @@ def depths(report, depth_df):
         with tabs.add_dropdown_menu():
             for ref_file, df_ref_file in depth_df.groupby("ref_file"):
                 # prepare data for depth vs coordinate plot
-                df_depth_vs_coords = df_ref_file.eval("step = end - start").eval(
-                    "total_mean_pos=step.cumsum() - step / 2"
+                df_depth_vs_coords = df_ref_file.eval("step = end - start")
+                # for each sample, get the mean position of each depth window (while
+                # concatenating all the sequences in that ref file)
+                df_depth_vs_coords = df_depth_vs_coords.groupby("sample_name").apply(
+                    lambda df: df.eval("total_mean_pos=step.cumsum() - step / 2")
                 )
                 # prepare data for cumulative depth plot
                 df_cumul_depth = get_relative_cumulative_depths(df_ref_file)

nextflow.config

@@ -51,7 +51,7 @@ manifest {
     description     = 'Align Nanopore reads and visualize mapping statistics.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.0.2'
+    version         = 'v1.0.3'
 }
 
 epi2melabs {