Plant-Food-Research-Open · GallVp · Oct 31, 2024 · Oct 31, 2024 · Oct 31, 2024
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 - [25-Oct-2024]
+## v2.2.0dev - [31-Oct-2024]
 
 ### `Added`
 
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 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)
 7. Added parameter `hic_samtools_ext_args` and set its default value to `-F 3852` [#159](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/159)
+8. Added the HiC QC report to the final report so that users don't have to navigate to the results folder [#162](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/162)
 
 ### `Fixed`
 

diff --git a/bin/report_modules/parsers/hic_parser.py b/bin/report_modules/parsers/hic_parser.py
@@ -15,28 +15,38 @@ def parse_hic_folder(folder_name="hic_outputs"):
         return {}
 
     list_of_hic_files = hic_folder_path.glob("*.html")
+    list_of_hic_files = [
+        x for x in list_of_hic_files if re.match(r"^\w+\.html$", x.name)
+    ]
 
     data = {"HIC": []}
 
     for hic_path in list_of_hic_files:
         hic_file_name = os.path.basename(str(hic_path))
 
-        file_tokens = re.findall(
+        tag = re.findall(
             r"([\w]+).html",
             hic_file_name,
         )[0]
 
-        labels_table = pd.read_csv(f"{folder_name}/{file_tokens}.agp.assembly", sep=" ")
-
+        # Get the labels table
+        labels_table = pd.read_csv(f"{folder_name}/{tag}.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)
 
+        # Get the HiC QC report
+        hicqc_report = [
+            x
+            for x in hic_folder_path.glob("*.pdf")
+            if re.match(rf"[\S]+\.on\.{tag}_qc_report\.pdf", x.name)
+        ][0]
+
         data["HIC"].append(
             {
-                "hap": file_tokens,
+                "hap": tag,
                 "hic_html_file_name": hic_file_name,
                 "labels_table": labels_table.to_dict("records"),
                 "labels_table_html": tabulate(
@@ -46,6 +56,7 @@ def parse_hic_folder(folder_name="hic_outputs"):
                     numalign="left",
                     showindex=False,
                 ),
+                "hicqc_report_pdf": os.path.basename(str(hicqc_report)),
             }
         )
 

diff --git a/bin/report_modules/templates/header.html b/bin/report_modules/templates/header.html
@@ -213,6 +213,18 @@
 
         .iframe-wrapper {
             text-align: center;
+            width: 90%;
+            margin-left: auto;
+            margin-right: auto;
+            margin-bottom: 32px;
+        }
+
+        .iframe-wrapper-hic {
+            width: 700px;
+            height: 850px;
+            margin-left: auto;
+            margin-right: auto;
+            margin-bottom: 32px;
         }
 
         .tab {

diff --git a/bin/report_modules/templates/hic/report_contents.html b/bin/report_modules/templates/hic/report_contents.html
@@ -5,14 +5,23 @@
     <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 class="iframe-wrapper-hic">
+      <iframe src="./hic/{{ all_stats_dicts['HIC'][item]['hic_html_file_name'] }}" width="700px" height="850px"></iframe>
     </div>
   </div>
   <div class="results-section">
+    <div class="section-para-wrapper">
+      <p class="section-para"><b>Sequence labels and lengths</b></p>
+    </div>
     <div class="table-outer">
       <div class="table-wrapper">{{ all_stats_dicts['HIC'][item]['labels_table_html'] }}</div>
     </div>
+    <div class="section-para-wrapper">
+      <p class="section-para"><b>HiC QC report</b></p>
+    </div>
+    <div class="iframe-wrapper">
+      <iframe src="./hic/hicqc/{{ all_stats_dicts['HIC'][item]['hicqc_report_pdf'] }}" width="100%" height="100%"></iframe>
+    </div>
   </div>
 </div>
 {% if vars.update({'is_first': False}) %} {% endif %} {% endfor %}
diff --git a/docs/images/hicqc.png b/docs/images/hicqc.png
diff --git a/docs/output.md b/docs/output.md
@@ -198,7 +198,12 @@ Kraken2 [assigns taxonomic labels](https://ccb.jhu.edu/software/kraken2/) to seq
 
 Hi-C contact mapping experiments measure the frequency of physical contact between loci in the genome. The resulting dataset, called a “contact map,” is represented using a [two-dimensional heatmap](https://github.com/igvteam/juicebox.js) where the intensity of each pixel indicates the frequency of contact between a pair of loci.
 
-<div align="center"><img src="images/hic_map.png" alt="AssemblyQC - HiC interactive contact map" width="50%"><hr><em>AssemblyQC - HiC interactive contact map</em></div>
+<div align="center">
+<img src="images/hicqc.png" alt="AssemblyQC - HiC QC report" width="44.59%">
+<img src="images/hic_map.png" alt="AssemblyQC - HiC interactive contact map" width="40%">
+<hr>
+<em>AssemblyQC - HiC results</em>
+</div>
 
 ### Synteny
 

diff --git a/subworkflows/local/fq2hic.nf b/subworkflows/local/fq2hic.nf
@@ -64,6 +64,7 @@ workflow FQ2HIC {
 
     HICQC ( ch_bam_and_ref.map { meta3, bam, fa -> [ meta3, bam ] } )
 
+    ch_hicqc_pdf                   = HICQC.out.pdf
     ch_versions                     = ch_versions.mix(HICQC.out.versions)
 
     // MODULE: MAKEAGPFROMFASTA | AGP2ASSEMBLY | ASSEMBLY2BEDPE
@@ -95,6 +96,7 @@ workflow FQ2HIC {
     ch_versions                     = ch_versions.mix(HIC2HTML.out.versions.first())
 
     emit:
+    hicqc_pdf                      = ch_hicqc_pdf
     hic                             = ch_hic
     html                            = HIC2HTML.out.html
     assembly                        = AGP2ASSEMBLY.out.assembly

diff --git a/workflows/assemblyqc.nf b/workflows/assemblyqc.nf
@@ -590,12 +590,16 @@ workflow ASSEMBLYQC {
         params.hic_skip_fastqc
     )
 
+    ch_hicqc_pdf                            = FQ2HIC.out.hicqc_pdf
     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 }
                                             )
+                                            | mix(
+                                                ch_hicqc_pdf.map { meta, pdf -> pdf }
+                                            )
     ch_versions                             = ch_versions.mix(FQ2HIC.out.versions)
 
     // SUBWORKFLOW: FASTA_SYNTENY