From ba423edc639b9b57a592a0d3590ddb65c0393d2f Mon Sep 17 00:00:00 2001
From: Kedi Cao <kedic715@gmail.com>
Date: Fri, 28 Mar 2025 15:51:56 +0100
Subject: [PATCH] save coverage analysis files for re-creating heatmaps
---
snakemodules/analysis.smk | 3 ++-
snakemodules/notebooks/contig_coverage_heatmap.py.ipynb | 3 ++-
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/snakemodules/analysis.smk b/snakemodules/analysis.smk
index 0806bef..babecad 100644
--- a/snakemodules/analysis.smk
+++ b/snakemodules/analysis.smk
@@ -482,7 +482,8 @@ rule coverage_analysis:
fasta = RESULTS_DIR + "/supercontigs.fa"
output:
RESULTS_DIR + "/heatmap_coverage.pdf",
- RESULTS_DIR + "/heatmap_coverage.txt"
+ RESULTS_DIR + "/heatmap_coverage.txt",
+ RESULTS_DIR + "/contigs_sorted_by_length.txt"
conda:
os.path.join(WORKFLOW_PATH,"snakemodules/envs/notebooks.yml")
benchmark:
diff --git a/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb b/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb
index d40567d..7e637e3 100644
--- a/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb
+++ b/snakemodules/notebooks/contig_coverage_heatmap.py.ipynb
@@ -215,7 +215,8 @@
"metadata": {},
"outputs": [],
"source": [
- "coverage_df_cleaned.to_csv(snakemake.output[1], sep='\\t', index=False)"
+ "coverage_df_cleaned.to_csv(snakemake.output[1], sep='\\t')\n",
+ "df_sort_contig.to_csv(snakemake.output[2],sep='\\t', index=False)"
]
},
{
--
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