Merge pull request #157 from Plant-Food-Research-Open/hic/seqlabels

Added a sequence labels table below the HiC contact map
Plant-Food-Research-Open · Oct 14, 2024 · 807ff31 · 807ff31
2 parents 789ae12 + af9a257
commit 807ff31
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.2.0dev - [10-Oct-2024]
+## v2.2.0dev - [15-Oct-2024]
 
 ### `Added`
 
@@ -12,14 +12,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 3. Updated `samtools faidx` to 1.21
 4. Now using nf-test for pipeline level testing [#153](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/153)
 5. Added `text/html` as content mime type for the report file [#146](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/146)
+6. Added a sequence labels table below the HiC contact map [#147](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/147)
 
 ### `Fixed`
 
 1. Fixed a bug where Gene score distribution graph did not appear correctly [#125](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/125)
 
 ### `Dependencies`
 
-1. Nextflow!>=23.04.0
+1. Nextflow!>=24.04.2
 2. [email protected]
 
 ### `Deprecated`

diff --git a/bin/report_modules/parsers/hic_parser.py b/bin/report_modules/parsers/hic_parser.py
@@ -1,5 +1,7 @@
 import os
 from pathlib import Path
+import pandas as pd
+from tabulate import tabulate
 import re
 
 from report_modules.parsers.parsing_commons import sort_list_of_results
@@ -24,10 +26,26 @@ def parse_hic_folder(folder_name="hic_outputs"):
             hic_file_name,
         )[0]
 
+        labels_table = pd.read_csv(f"{folder_name}/{file_tokens}.agp.assembly", sep=" ")
+
+        labels_table = labels_table[labels_table.iloc[:, 0].str.startswith(">")].iloc[
+            :, [0, 2]
+        ]
+        labels_table.columns = ["Sequence", "Length"]
+        labels_table.Length = labels_table.Length.astype(int)
+
         data["HIC"].append(
             {
                 "hap": file_tokens,
                 "hic_html_file_name": hic_file_name,
+                "labels_table": labels_table.to_dict("records"),
+                "labels_table_html": tabulate(
+                    labels_table,
+                    headers=["Sequence", "Length"],
+                    tablefmt="html",
+                    numalign="left",
+                    showindex=False,
+                ),
             }
         )
 

diff --git a/bin/report_modules/templates/hic/report_contents.html b/bin/report_modules/templates/hic/report_contents.html
@@ -1,17 +1,18 @@
 {% set vars = {'is_first': True} %} {% for item in range(all_stats_dicts["HIC"]|length) %} {% set active_text =
 'display: block' if vars.is_first else 'display: none' %}
 <div id="tabcontent_HIC_{{ all_stats_dicts['HIC'][item]['hap'] }}" class="tabcontent-HIC" style="{{ active_text }}">
-    <div class="results-section">
-        <div class="section-heading-wrapper">
-            <div class="section-heading">{{ all_stats_dicts['HIC'][item]['hap'] }}</div>
-        </div>
-        <div class="iframe-wrapper">
-            <iframe
-                src="./hic/{{ all_stats_dicts['HIC'][item]['hic_html_file_name'] }}"
-                width="100%"
-                height="100%"
-            ></iframe>
-        </div>
+  <div class="results-section">
+    <div class="section-heading-wrapper">
+      <div class="section-heading">{{ all_stats_dicts['HIC'][item]['hap'] }}</div>
     </div>
+    <div class="iframe-wrapper">
+      <iframe src="./hic/{{ all_stats_dicts['HIC'][item]['hic_html_file_name'] }}" width="100%" height="100%"></iframe>
+    </div>
+  </div>
+  <div class="results-section">
+    <div class="table-outer">
+      <div class="table-wrapper">{{ all_stats_dicts['HIC'][item]['labels_table_html'] }}</div>
+    </div>
+  </div>
 </div>
 {% if vars.update({'is_first': False}) %} {% endif %} {% endfor %}
diff --git a/subworkflows/local/fq2hic.nf b/subworkflows/local/fq2hic.nf
@@ -97,5 +97,6 @@ workflow FQ2HIC {
     emit:
     hic                             = ch_hic
     html                            = HIC2HTML.out.html
+    assembly                        = AGP2ASSEMBLY.out.assembly
     versions                        = ch_versions
 }
diff --git a/workflows/assemblyqc.nf b/workflows/assemblyqc.nf
@@ -591,6 +591,11 @@ workflow ASSEMBLYQC {
     )
 
     ch_hic_html                             = FQ2HIC.out.html
+    ch_hic_assembly                         = FQ2HIC.out.assembly
+    ch_hic_report_files                     = ch_hic_html
+                                            | mix(
+                                                ch_hic_assembly.map { tag, assembly -> assembly }
+                                            )
     ch_versions                             = ch_versions.mix(FQ2HIC.out.versions)
 
     // SUBWORKFLOW: FASTA_SYNTENY
@@ -822,7 +827,7 @@ workflow ASSEMBLYQC {
         ch_tidk_outputs                     .collect().ifEmpty([]),
         ch_lai_outputs                      .collect().ifEmpty([]),
         ch_kraken2_plot                     .collect().ifEmpty([]),
-        ch_hic_html                         .collect().ifEmpty([]),
+        ch_hic_report_files                 .collect().ifEmpty([]),
         ch_synteny_outputs                  .collect().ifEmpty([]),
         ch_merqury_outputs                  .collect().ifEmpty([]),
         ch_versions_yml,