Added orthofinder

Plant-Food-Research-Open · Nov 2, 2024 · 2e8844d · 2e8844d
1 parent d410971
commit 2e8844d
Show file tree

Hide file tree

Showing 32 changed files with 1,521 additions and 63 deletions.
diff --git a/README.md b/README.md
@@ -16,61 +16,7 @@
 
 ## Pipeline Flowchart
 
-```mermaid
-%%{init: {
-    'theme': 'base',
-    'themeVariables': {
-    'fontSize': '52px",
-    'primaryColor': '#9A6421',
-    'primaryTextColor': '#ffffff',
-    'primaryBorderColor': '#9A6421',
-    'lineColor': '#B180A8',
-    'secondaryColor': '#455C58',
-    'tertiaryColor': '#ffffff'
-  }
-}}%%
-flowchart LR
-  forEachTag(Assembly) ==> VALIDATE_FORMAT[VALIDATE FORMAT]
-
-  VALIDATE_FORMAT ==> ncbiFCS[<span style="white-space: nowrap;">NCBI FCS ADAPTOR</span>]
-  ncbiFCS ==> Check{Check}
-
-  VALIDATE_FORMAT ==> ncbiGX[<span style="white-space: nowrap;">NCBI FCS GX</span>]
-  ncbiGX ==> Check
-  Check ==> |Clean|Run(Run)
-
-  Check ==> |Contamination|Skip(Skip All)
-  Skip ==> REPORT
-
-  VALIDATE_FORMAT ==> GFF_STATS[<span style="white-space: nowrap;">GENOMETOOLS GT STAT</span>]
-
-  Run ==> ASS_STATS[<span style="white-space: nowrap;">STATS</span>]
-  Run ==> BUSCO
-  Run ==> TIDK
-  Run ==> LAI
-  Run ==> KRAKEN2
-  Run ==> HIC_CONTACT_MAP[<span style="white-space: nowrap;">HIC CONTACT MAP</span>]
-  Run ==> MUMMER
-  Run ==> MINIMAP2
-  Run ==> MERQURY
-
-  MUMMER ==> CIRCOS
-  MUMMER ==> DOTPLOT
-
-  MINIMAP2 ==> PLOTSR
-
-  ASS_STATS ==> REPORT
-  GFF_STATS ==> REPORT
-  BUSCO ==> REPORT
-  TIDK ==> REPORT
-  LAI ==> REPORT
-  KRAKEN2 ==> REPORT
-  HIC_CONTACT_MAP ==> REPORT
-  CIRCOS ==> REPORT
-  DOTPLOT ==> REPORT
-  PLOTSR ==> REPORT
-  MERQURY ==> REPORT
-```
+<p align="center"><img src="docs/images/assemblyqc.png"></p>
 
 - [FASTA VALIDATOR](https://github.com/linsalrob/fasta_validator) + [SEQKIT RMDUP](https://github.com/shenwei356/seqkit): FASTA validation
 - [GENOMETOOLS GT GFF3VALIDATOR](https://genometools.org/tools/gt_gff3validator.html): GFF3 validation
@@ -85,6 +31,7 @@ flowchart LR
 - [HIC CONTACT MAP](https://github.com/igvteam/juicebox.js): Alignment and visualisation of HiC data
 - [MUMMER](https://github.com/mummer4/mummer) → [CIRCOS](http://circos.ca/documentation/) + [DOTPLOT](https://plotly.com) & [MINIMAP2](https://github.com/lh3/minimap2) → [PLOTSR](https://github.com/schneebergerlab/plotsr): Synteny analysis
 - [MERQURY](https://github.com/marbl/merqury): K-mer completeness, consensus quality and phasing assessment
+- [ORTHOFINDER](https://github.com/davidemms/OrthoFinder): Phylogenetic orthology inference for comparative genomics
 
 ## Usage
 
@@ -140,31 +87,32 @@ The pipeline uses nf-core modules contributed by following authors:
 
 <a href="https://github.com/gallvp"><img src="https://github.com/gallvp.png" width="50" height="50"></a>
 <a href="https://github.com/drpatelh"><img src="https://github.com/drpatelh.png" width="50" height="50"></a>
-<a href="https://github.com/midnighter"><img src="https://github.com/midnighter.png" width="50" height="50"></a>
 <a href="https://github.com/mahesh-panchal"><img src="https://github.com/mahesh-panchal.png" width="50" height="50"></a>
 <a href="https://github.com/jfy133"><img src="https://github.com/jfy133.png" width="50" height="50"></a>
-<a href="https://github.com/adamrtalbot"><img src="https://github.com/adamrtalbot.png" width="50" height="50"></a>
+<a href="https://github.com/midnighter"><img src="https://github.com/midnighter.png" width="50" height="50"></a>
+<a href="https://github.com/joseespinosa"><img src="https://github.com/joseespinosa.png" width="50" height="50"></a>
+<a href="https://github.com/sofstam"><img src="https://github.com/sofstam.png" width="50" height="50"></a>
+<a href="https://github.com/sateeshperi"><img src="https://github.com/sateeshperi.png" width="50" height="50"></a>
 <a href="https://github.com/maxulysse"><img src="https://github.com/maxulysse.png" width="50" height="50"></a>
 <a href="https://github.com/matthdsm"><img src="https://github.com/matthdsm.png" width="50" height="50"></a>
-<a href="https://github.com/joseespinosa"><img src="https://github.com/joseespinosa.png" width="50" height="50"></a>
+<a href="https://github.com/heuermh"><img src="https://github.com/heuermh.png" width="50" height="50"></a>
 <a href="https://github.com/grst"><img src="https://github.com/grst.png" width="50" height="50"></a>
+<a href="https://github.com/fellen31"><img src="https://github.com/fellen31.png" width="50" height="50"></a>
 <a href="https://github.com/ewels"><img src="https://github.com/ewels.png" width="50" height="50"></a>
-<a href="https://github.com/sofstam"><img src="https://github.com/sofstam.png" width="50" height="50"></a>
-<a href="https://github.com/sateeshperi"><img src="https://github.com/sateeshperi.png" width="50" height="50"></a>
+<a href="https://github.com/edmundmiller"><img src="https://github.com/edmundmiller.png" width="50" height="50"></a>
+<a href="https://github.com/adamrtalbot"><img src="https://github.com/adamrtalbot.png" width="50" height="50"></a>
 <a href="https://github.com/robsyme"><img src="https://github.com/robsyme.png" width="50" height="50"></a>
 <a href="https://github.com/priyanka-surana"><img src="https://github.com/priyanka-surana.png" width="50" height="50"></a>
 <a href="https://github.com/phue"><img src="https://github.com/phue.png" width="50" height="50"></a>
+<a href="https://github.com/nvnieuwk"><img src="https://github.com/nvnieuwk.png" width="50" height="50"></a>
 <a href="https://github.com/muffato"><img src="https://github.com/muffato.png" width="50" height="50"></a>
 <a href="https://github.com/lescai"><img src="https://github.com/lescai.png" width="50" height="50"></a>
 <a href="https://github.com/kevinmenden"><img src="https://github.com/kevinmenden.png" width="50" height="50"></a>
 <a href="https://github.com/jvhagey"><img src="https://github.com/jvhagey.png" width="50" height="50"></a>
 <a href="https://github.com/jeremy1805"><img src="https://github.com/jeremy1805.png" width="50" height="50"></a>
-<a href="https://github.com/heuermh"><img src="https://github.com/heuermh.png" width="50" height="50"></a>
 <a href="https://github.com/friederikehanssen"><img src="https://github.com/friederikehanssen.png" width="50" height="50"></a>
-<a href="https://github.com/fellen31"><img src="https://github.com/fellen31.png" width="50" height="50"></a>
 <a href="https://github.com/felixkrueger"><img src="https://github.com/felixkrueger.png" width="50" height="50"></a>
 <a href="https://github.com/erikrikarddaniel"><img src="https://github.com/erikrikarddaniel.png" width="50" height="50"></a>
-<a href="https://github.com/edmundmiller"><img src="https://github.com/edmundmiller.png" width="50" height="50"></a>
 <a href="https://github.com/d4straub"><img src="https://github.com/d4straub.png" width="50" height="50"></a>
 <a href="https://github.com/charles-plessy"><img src="https://github.com/charles-plessy.png" width="50" height="50"></a>
 

diff --git a/bin/assemblyqc.py b/bin/assemblyqc.py
@@ -29,6 +29,7 @@
 from report_modules.parsers.hic_parser import parse_hic_folder
 from report_modules.parsers.synteny_parser import parse_synteny_folder
 from report_modules.parsers.merqury_parser import parse_merqury_folder
+from report_modules.parsers.orthofinder_parser import parse_orthofinder_folder
 
 if __name__ == "__main__":
     params_dict, params_table = parse_params_json("params_json.json")
@@ -57,6 +58,7 @@
     data_from_tools = {**data_from_tools, **parse_hic_folder()}
     data_from_tools = {**data_from_tools, **parse_synteny_folder()}
     data_from_tools = {**data_from_tools, **parse_merqury_folder()}
+    data_from_tools = {**data_from_tools, **parse_orthofinder_folder()}
 
     with open("software_versions.yml", "r") as f:
         versions_from_ch_versions = yaml.safe_load(f)

diff --git a/bin/report_modules/parsers/orthofinder_parser.py b/bin/report_modules/parsers/orthofinder_parser.py
@@ -0,0 +1,100 @@
+import pandas as pd
+import base64
+import os
+import re
+
+import matplotlib.pyplot as plt
+from tabulate import tabulate
+from pathlib import Path
+from io import StringIO
+from Bio import Phylo
+
+
+def parse_orthofinder_folder(folder_name="orthofinder_outputs/assemblyqc"):
+    dir = os.getcwdb().decode()
+    results_root_path = Path(f"{dir}/{folder_name}")
+
+    if not results_root_path.exists():
+        return {}
+
+    data = {"ORTHOFINDER": {}}
+
+    # Species tree
+    tree = Phylo.read(
+        f"{results_root_path}/Species_Tree/SpeciesTree_rooted.txt", "newick"
+    )
+
+    fig = plt.figure(figsize=(6, 6))
+    ax = fig.add_subplot(1, 1, 1)
+    Phylo.draw(tree, do_show=False, axes=ax)
+
+    plt.gca().spines["top"].set_visible(False)
+    plt.gca().spines["right"].set_visible(False)
+
+    plt.savefig("speciestree_rooted.png", format="png", dpi=300)
+
+    with open("speciestree_rooted.png", "rb") as f:
+        binary_fc = f.read()
+
+    base64_utf8_str = base64.b64encode(binary_fc).decode("utf-8")
+    data["ORTHOFINDER"]["speciestree_rooted"] = (
+        f"data:image/png+xml;base64,{base64_utf8_str}"
+    )
+
+    # Overall statistics
+    overall_statistics = Path(
+        f"{results_root_path}/Comparative_Genomics_Statistics/Statistics_Overall.tsv"
+    ).read_text()
+
+    ## General stats
+    general_stats = re.findall(
+        r"(Number of species.*)Orthogroups file", overall_statistics, flags=re.DOTALL
+    )[0]
+    general_stats_pd = pd.read_csv(StringIO(general_stats), sep="\t")
+
+    data["ORTHOFINDER"]["general_stats"] = general_stats_pd.to_dict("records")
+    data["ORTHOFINDER"]["general_stats_html"] = tabulate(
+        general_stats_pd,
+        headers=["Stat", "Value"],
+        tablefmt="html",
+        numalign="left",
+        showindex=False,
+    )
+
+    ## Genes per-species
+    genes_per_species = re.findall(
+        r"(Average number of genes per-species in orthogroup.*)Number of species in orthogroup",
+        overall_statistics,
+        flags=re.DOTALL,
+    )[0]
+    genes_per_species_pd = pd.read_csv(StringIO(genes_per_species), sep="\t", header=0)
+    data["ORTHOFINDER"]["genes_per_species"] = genes_per_species_pd.to_dict("records")
+    data["ORTHOFINDER"]["genes_per_species_html"] = tabulate(
+        genes_per_species_pd,
+        headers=genes_per_species_pd.columns.to_list(),
+        tablefmt="html",
+        numalign="left",
+        showindex=False,
+    )
+
+    ## Number of species in orthogroup
+    num_species_orthogroup = re.findall(
+        r"(Number of species in orthogroup.*)",
+        overall_statistics,
+        flags=re.DOTALL,
+    )[0]
+    num_species_orthogroup_pd = pd.read_csv(
+        StringIO(num_species_orthogroup), sep="\t", header=0
+    )
+    data["ORTHOFINDER"]["num_species_orthogroup"] = num_species_orthogroup_pd.to_dict(
+        "records"
+    )
+    data["ORTHOFINDER"]["num_species_orthogroup_html"] = tabulate(
+        num_species_orthogroup_pd,
+        headers=num_species_orthogroup_pd.columns.to_list(),
+        tablefmt="html",
+        numalign="left",
+        showindex=False,
+    )
+
+    return data
diff --git a/bin/report_modules/templates/base.html b/bin/report_modules/templates/base.html
@@ -79,6 +79,11 @@
     {% if 'MERQURY' in all_stats_dicts %}
     <button class="tablinks" onclick="openTool(event, 'MERQURY')">MERQURY</button>
     {% endif %}
+
+    {% if 'ORTHOFINDER' in all_stats_dicts %}
+    <button class="tablinks" onclick="openTool(event, 'ORTHOFINDER')">ORTHOFINDER</button>
+    {% endif %}
+
   </div>
 
   {% include 'params/params.html' %}
@@ -151,6 +156,11 @@
   {% if 'MERQURY' in all_stats_dicts %}
   {% include 'merqury/merqury.html' %}
   {% endif %}
+
+  {% if 'ORTHOFINDER' in all_stats_dicts %}
+  {% include 'orthofinder/orthofinder.html' %}
+  {% endif %}
+
 </body>
 {% include 'js.html' %}
 

diff --git a/bin/report_modules/templates/orthofinder/orthofinder.html b/bin/report_modules/templates/orthofinder/orthofinder.html
@@ -0,0 +1,14 @@
+<div id="ORTHOFINDER" class="tabcontent" style="display: none">
+  <div class="section-para-wrapper">
+    <p class="section-para">
+      A tool for phylogenetic orthology inference for comparative genomics.
+    </p>
+    <p class="section-para"><b>Reference:</b></p>
+    <p class="section-para">
+      Emms, D.M., Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 20, 238
+      (2019). <a href="https://doi.org/10.1186/s13059-019-1832-y" target="_blank">10.1186/s13059-019-1832-y</a>
+    </p>
+    <p class="section-para"><b>Version: {{ all_stats_dicts['VERSIONS']['ORTHOFINDER']['orthofinder'] }}</b></p>
+  </div>
+  {% include 'orthofinder/report_contents.html' %}
+</div>
diff --git a/bin/report_modules/templates/orthofinder/report_contents.html b/bin/report_modules/templates/orthofinder/report_contents.html
@@ -0,0 +1,33 @@
+<div id="tabcontent_ORTHOFINDER" class="tabcontent-ORTHOFINDER" style="display: block">
+  <div class="results-section">
+
+    <div class="section-para-wrapper">
+      <p class="section-para"><b>Species tree (rooted)</b></p>
+    </div>
+    <div class="image-wrapper" style="width: 60%;margin-left: auto;margin-right: auto;">
+      <img src="{{ all_stats_dicts['ORTHOFINDER']['speciestree_rooted'] }}" alt="" />
+    </div>
+
+    <div class="section-para-wrapper">
+      <p class="section-para"><b>General statistics</b></p>
+    </div>
+    <div class="table-outer">
+      <div class="table-wrapper">{{ all_stats_dicts['ORTHOFINDER']['general_stats_html'] }}</div>
+    </div>
+
+    <div class="section-para-wrapper">
+      <p class="section-para"><b>Genes per-species in orthogroup</b></p>
+    </div>
+    <div class="table-outer">
+      <div class="table-wrapper">{{ all_stats_dicts['ORTHOFINDER']['genes_per_species_html'] }}</div>
+    </div>
+
+    <div class="section-para-wrapper">
+      <p class="section-para"><b>Number of species in orthogroup</b></p>
+    </div>
+    <div class="table-outer">
+      <div class="table-wrapper">{{ all_stats_dicts['ORTHOFINDER']['num_species_orthogroup_html'] }}</div>
+    </div>
+
+  </div>
+</div>
diff --git a/conf/modules.config b/conf/modules.config
@@ -388,6 +388,18 @@ process {
         ]
     }
 
+    withName: '.*:ASSEMBLYQC:GFFREAD' {
+        ext.args = '-y -S'
+    }
+
+    withName: '.*:ASSEMBLYQC:ORTHOFINDER' {
+        publishDir = [
+            path: { "${params.outdir}/orthofinder" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
+        ]
+    }
+
     withName: '.*:ASSEMBLYQC:CREATEREPORT' {
         publishDir = [
             [

diff --git a/docs/images/assemblyqc.png b/docs/images/assemblyqc.png
diff --git a/docs/parameters.md b/docs/parameters.md
@@ -100,6 +100,12 @@ A Nextflow pipeline which evaluates assembly quality with multiple QC tools and
 | `merqury_skip`        | Skip merqury analysis            | `boolean` | True    |          |        |
 | `merqury_kmer_length` | kmer length for merqury analysis | `integer` | 21      |          |        |
 
+## Orthofinder options
+
+| Parameter          | Description      | Type      | Default | Required | Hidden |
+| ------------------ | ---------------- | --------- | ------- | -------- | ------ |
+| `orthofinder_skip` | Skip orthofinder | `boolean` | True    |          |        |
+
 ## Institutional config options
 
 Parameters used to describe centralised config profiles. These should not be edited.

diff --git a/modules.json b/modules.json
@@ -180,6 +180,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "gffread": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -210,6 +215,11 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
+                    "orthofinder": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "seqkit/rmdup": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",

diff --git a/modules/local/createreport.nf b/modules/local/createreport.nf
@@ -20,6 +20,7 @@ process CREATEREPORT {
     path hic_outputs                , stageAs: 'hic_outputs/*'
     path synteny_outputs            , stageAs: 'synteny_outputs/*'
     path merqury_outputs            , stageAs: 'merqury_outputs/*'
+    path orthofinder_outputs        , stageAs: 'orthofinder_outputs/*'
     path versions
     val params_json
     val params_summary_json

diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml