Add more support for customizing coverage plot

bin/plot-coverage.py

@@ -125,7 +125,7 @@ def plot_coverage(depths: pd.DataFrame, bed: dict, sample_name: str="Sample", th
     longest_chrom_length = depths[depths.chrom == longest_chrom].pos.max()
     longest_chrom_length_mb = longest_chrom_length / 1_000_000
     sns.set_style("whitegrid")
-    dpi = 100
+    dpi = 300
     width_pixels = round(longest_chrom_length_mb * width_inches_per_mb * dpi)
     height_pixels = round(height_inches_per_chrom * num_chroms * dpi)
     logging.info(f"Plot size: {width_pixels} x {height_pixels} pixels")

modules/alignment_variants.nf

@@ -418,12 +418,18 @@ process plot_coverage {
     tuple val(sample_id), path("${sample_id}_${short_long}_coverage.png"), optional: true
 
     script:
+    log_scale = params.coverage_plot_log_scale ? "--log-scale" : ""
     """
     plot-coverage.py \
 	--sample-id ${sample_id} \
 	--ref ${ref} \
 	--depths ${depths} \
 	--threshold ${params.min_depth} \
+	--y-limit ${params.coverage_plot_y_limit} \
+	--width-inches-per-mb ${params.coverage_plot_width_inches_per_mb} \
+	--height-inches-per-chrom ${params.coverage_plot_height_inches_per_chrom} \
+	--window ${params.coverage_plot_window_size} \
+	${log_scale} \
 	--output ${sample_id}_${short_long}_coverage.png
 	
     """

nextflow.config

@@ -27,6 +27,11 @@ params {
     min_alternate_fraction_for_variant_calling = 0.1
     qualimap_coverage_histogram_limit = 100
     coverage_by_depth_limit = 500
+    coverage_plot_y_limit = 500
+    coverage_plot_log_scale = false
+    coverage_plot_width_inches_per_mb = 3
+    coverage_plot_height_inches_per_chrom = 2
+    coverage_plot_window_size = 1000
     qualimap_memory = '4G'
     skip_alignment_cleaning = false
     align_long_reads = false