From 3d82a85af0dbaf9973dfe9159815dea1f55e7022 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <johan@biocommons.org.au>
Date: Mon, 15 Apr 2024 15:49:07 +0930
Subject: [PATCH 01/15] Add GoogleSheet import feature from field guide

---
 .github/workflows/jekyll.yml       | 32 ++++++++++++++++++++
 index.md                           |  2 ++
 requirements.txt                   |  6 ++++
 scripts/guides_table_conversion.py | 47 ++++++++++++++++++++++++++++++
 4 files changed, 87 insertions(+)
 create mode 100644 requirements.txt
 create mode 100644 scripts/guides_table_conversion.py

diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
index dae187b..980cf2c 100644
--- a/.github/workflows/jekyll.yml
+++ b/.github/workflows/jekyll.yml
@@ -13,6 +13,38 @@ permissions:
   id-token: write
 
 jobs:
+
+  update_guides:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8.16'
+
+      - name: install python packages
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: execute table conversion script
+        run: python scripts/guides_table_conversion.py
+
+      - name: Commit if updated
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add -A
+          git diff-index --quiet HEAD || git commit -m "update guides"
+
+      - name: Push if changes
+        uses: ad-m/github-push-action@v0.6.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: main
+
   build:
     runs-on: ubuntu-latest
     steps:
diff --git a/index.md b/index.md
index f02fafd..87fe472 100644
--- a/index.md
+++ b/index.md
@@ -20,6 +20,8 @@ If you have an idea for a new How-to Guide, or a new category, please visit the
 
 ## Acknowledgements
 
+The authors would like to acknowledge Marion Shadbolt (@mshadbolt) for developing the GoogleSheet import and parsing that is being reused for the How-to Hub.
+
 This work is supported by the [Australian BioCommons](https://www.biocommons.org.au/) via funding from [Bioplatforms Australia](https://bioplatforms.com/), the Australian Research Data Commons (https://doi.org/10.47486/PL105) and the Queensland Government Research Infrastructure Co-investment Fund (RICF) programme. Bioplatforms Australia and the Australian Research Data Commons are funded by the National Collaborative Research Infrastructure Strategy (NCRIS).
 
 This guide makes use of the [ELIXIR toolkit theme](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme)
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..99d66ab
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,6 @@
+pandas
+requests
+argparse
+PyYAML
+python-frontmatter
+urllib3
\ No newline at end of file
diff --git a/scripts/guides_table_conversion.py b/scripts/guides_table_conversion.py
new file mode 100644
index 0000000..0681e4c
--- /dev/null
+++ b/scripts/guides_table_conversion.py
@@ -0,0 +1,47 @@
+"""
+Adapted from https://github.com/elixir-europe/rdmkit/blob/master/var/conversions.py
+Adapted from https://github.com/AustralianBioCommons/human-omics-data-sharing-field-guide/blob/328e84634d10b0df51e798dbf1cc114c7cb26357/var/tools_table_conversion.py
+"""
+
+import pandas as pd
+import yaml
+import os
+
+# --------- Variables ---------
+
+google_id = "1CWSW5CAg0f8e5XB9Bl80jiDT8QCWOWhuCxKjDWLi5a4"
+gid = "0"
+url = f"https://docs.google.com/spreadsheets/d/{google_id}/export?format=csv&gid={gid}"
+output_path = "_data/tool_and_resource_list.yml"
+rootdir = '../pages'
+allowed_registries = ['biotools', 'fairsharing', 'tess', 'wfh-collection', 'wfh', 'doi', 'template']
+
+# --------- Converting the table ---------
+
+print(f"----> Converting GoogleSheets table to {output_path} started.")
+resource_table = pd.read_csv(url, dtype={'name': str, 'url': str, 'description': str, 'id': str, 'fairsharing': str,
+                                         'biotools': str, 'tess': str, 'wfh-collection': str, 'wfh': str,
+                                         'doi': str, 'template': str, 'categories': str})
+resource_list = resource_table.to_dict("records")
+clean_resource_list = []
+for resource in resource_list:
+    if not pd.isna(resource['categories']):
+        category_list = resource['categories'].rsplit(sep=",")
+    else:
+        category_list = ""
+    registry_dict = {}
+    for registry in allowed_registries:
+        if not pd.isna(resource[registry]):
+            registry_dict[registry] = resource[registry]
+        del(resource[registry])
+    clean_resource = {k: resource[k] for k in resource if not pd.isna(resource[k])}
+    clean_resource_list.append(clean_resource)
+    clean_resource['registry'] = registry_dict
+    if category_list != "":
+        clean_resource['categories'] = category_list
+
+print(os.getcwd())
+with open(output_path, 'w+') as yaml_file:
+    documents = yaml.dump(clean_resource_list, yaml_file)
+
+print("----> YAML is dumped successfully")
\ No newline at end of file

From 10a30c8eef9ac2a39ff8e3b8834e7820e6158a18 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <johan@biocommons.org.au>
Date: Mon, 15 Apr 2024 15:55:16 +0930
Subject: [PATCH 02/15] Update jekyll.yml

---
 .github/workflows/jekyll.yml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
index 980cf2c..1523679 100644
--- a/.github/workflows/jekyll.yml
+++ b/.github/workflows/jekyll.yml
@@ -7,11 +7,6 @@ on:
     branches: [ main, master ]
   workflow_dispatch:
 
-permissions:
-  contents: read
-  pages: write
-  id-token: write
-
 jobs:
 
   update_guides:

From 54b25ca87708c64fcdf5fbe3e27a151500c04330 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Mon, 15 Apr 2024 06:25:51 +0000
Subject: [PATCH 03/15] update guides

---
 _data/tool_and_resource_list.yml | 54 ++++++--------------------------
 1 file changed, 9 insertions(+), 45 deletions(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index 98752ec..7fc6272 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -1,49 +1,13 @@
-- id: genome-assembly-hifi
-  description:
-    This How-to-Guide describes the steps required to assemble your genome on the Galaxy Australia platform, using multiple workflows developed in consultation between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia, and the Australian BioCommons.
-  url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
+- categories:
+  - genome assembly
+  - documentation
+  description: This How-to-Guide describes the steps required to assemble your genome
+    on the Galaxy Australia platform, using multiple workflows developed in consultation
+    between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia,
+    and the Australian BioCommons.
+  id: genome-assembly-hifi
   name: Genome assembly with `hifiasm` on Galaxy Australia
   registry:
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
-  related_pages:
-    - genome_assembly
-- id: genome-assembly-qc
-  description:
-    Once a genome has been assembled, it is important to assess the quality of the assembly, and in the first instance, this quality control (QC) can be achieved using the workflow described here.
-  url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/assembly_qc
-  name: Assess the quality of your genome assembly
-  registry:
-    tess: genome assembly
-    wfh: https://workflowhub.eu/workflows/403
-  related_pages:
-    - genome_assembly
-- id: how-to-create-guide
-  description:
-    This web page describes How-to create new How-to Guide websites using a GitHub repository template.
-  url: https://australianbiocommons.github.io/how-to-guide-template/
-  name: How-to Guide for creating a How-to Guide
-  related_pages:
-    - documentation
-  registry:
-    doi: https://doi.org/10.5281/zenodo.8210268
-    template: https://github.com/AustralianBioCommons/guide-template
-- id: doc-guidelines
-  description:
-    The Australian BioCommons has been working with community bioinformaticians and our infrastructure partners to establish a guidelines repository that can act as a template for documentation of tools and workflows.
-  url: https://australianbiocommons.github.io/how-to-doc-guidelines/
-  name: How-to use the Australian BioCommons documentation guidelines
-  related_pages:
-    - documentation
-  registry:
-    template: https://github.com/AustralianBioCommons/doc_guidelines
-- id: stacks
-  description:
-    This How-to Guide describes the steps required to run the Stacks workflows on Galaxy Australia to analyse RADseq data, using workflows developed in consultations between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia, and the Australian BioCommons.
-  url: https://australianbiocommons.github.io/how-to-guides/stacks_workflows/stacks
-  name: Stacks workflows in Galaxy Australia using RADseq
-  registry:
-    biotools: stacks
-    tess: RAD seq
-  related_pages:
-    - pop_gen
\ No newline at end of file
+  url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly

From 16844de195d08d0c60733dae0fa1780a2faa0289 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 17 Apr 2024 00:04:59 +0000
Subject: [PATCH 04/15] update guides

---
 _data/tool_and_resource_list.yml | 53 +++++++++++++++++++++++++++++++-
 1 file changed, 52 insertions(+), 1 deletion(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index 7fc6272..49ca841 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -1,6 +1,5 @@
 - categories:
   - genome assembly
-  - documentation
   description: This How-to-Guide describes the steps required to assemble your genome
     on the Galaxy Australia platform, using multiple workflows developed in consultation
     between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia,
@@ -11,3 +10,55 @@
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
+- categories:
+  - genome assembly
+  description: Once a genome has been assembled, it is important to assess the quality
+    of the assembly, and in the first instance, this quality control (QC) can be achieved
+    using the workflow described here.
+  id: genome-assembly-qc
+  name: Assess the quality of your genome assembly
+  registry:
+    tess: genome assembly
+    wfh: https://workflowhub.eu/workflows/403
+  url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/assembly_qc
+- categories:
+  - documentation
+  description: This web page describes How-to create new How-to Guide websites using
+    a GitHub repository template.
+  id: how-to-create-guide
+  name: How-to Guide for creating a How-to Guide
+  registry:
+    doi: https://doi.org/10.5281/zenodo.8210268
+    template: https://github.com/AustralianBioCommons/guide-template
+  url: https://australianbiocommons.github.io/how-to-guide-template/
+- categories:
+  - documentation
+  description: The Australian BioCommons has been working with community bioinformaticians
+    and our infrastructure partners to establish a guidelines repository that can
+    act as a template for documentation of tools and workflows.
+  id: doc-guidelines
+  name: How-to use the Australian BioCommons documentation guidelines
+  registry:
+    template: https://github.com/AustralianBioCommons/doc_guidelines
+  url: https://australianbiocommons.github.io/how-to-doc-guidelines/
+- categories:
+  - pop_gen
+  description: This How-to Guide describes the steps required to run the Stacks workflows
+    on Galaxy Australia to analyse RADseq data, using workflows developed in consultations
+    between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia,
+    and the Australian BioCommons.
+  id: stacks
+  name: Stacks workflows in Galaxy Australia using RADseq
+  registry:
+    biotools: stacks
+    tess: RAD seq
+  url: https://australianbiocommons.github.io/how-to-guides/stacks_workflows/stacks
+- categories:
+  - metagenomics
+  description: This How-to Guide describes how to use the shotgun metagenomics workflow
+    with MetaPhlAn2 on Galaxy Australia. The workflow is using the tools MetaPhlAn2
+    for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes.
+  id: shotgun-metagenomics-metaphlanv2
+  name: Shotgun metagenomics workflow with MetaPhlAn2 on Galaxy Australia
+  registry: {}
+  url: https://vmurigneu.github.io/shotgun_howto_ga_workflows/shotgun_wf_guide

From 5258f9a97f8513a31e536b78f3afa0397026c451 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <50811354+supernord@users.noreply.github.com>
Date: Wed, 17 Apr 2024 09:54:53 +0930
Subject: [PATCH 05/15] Update jekyll.yml

---
 .github/workflows/jekyll.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
index 1523679..413634c 100644
--- a/.github/workflows/jekyll.yml
+++ b/.github/workflows/jekyll.yml
@@ -7,6 +7,9 @@ on:
     branches: [ main, master ]
   workflow_dispatch:
 
+permissions:
+  id-token: write
+
 jobs:
 
   update_guides:

From 13ab61e040fa733070d961154c4dbd7a71c70197 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <johan@biocommons.org.au>
Date: Wed, 17 Apr 2024 14:29:34 +0930
Subject: [PATCH 06/15] Add update_guides.yml

---
 .github/workflows/jekyll.yml        | 33 ++---------------------
 .github/workflows/update_guides.yml | 41 +++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 31 deletions(-)
 create mode 100644 .github/workflows/update_guides.yml

diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
index 413634c..ea45470 100644
--- a/.github/workflows/jekyll.yml
+++ b/.github/workflows/jekyll.yml
@@ -8,41 +8,12 @@ on:
   workflow_dispatch:
 
 permissions:
+  contents: read
+  pages: write
   id-token: write
 
 jobs:
 
-  update_guides:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v3
-
-      - name: setup python
-        uses: actions/setup-python@v2
-        with:
-          python-version: '3.8.16'
-
-      - name: install python packages
-        run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
-
-      - name: execute table conversion script
-        run: python scripts/guides_table_conversion.py
-
-      - name: Commit if updated
-        run: |
-          git config --local user.email "action@github.com"
-          git config --local user.name "GitHub Action"
-          git add -A
-          git diff-index --quiet HEAD || git commit -m "update guides"
-
-      - name: Push if changes
-        uses: ad-m/github-push-action@v0.6.0
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          branch: main
-
   build:
     runs-on: ubuntu-latest
     steps:
diff --git a/.github/workflows/update_guides.yml b/.github/workflows/update_guides.yml
new file mode 100644
index 0000000..44bbb13
--- /dev/null
+++ b/.github/workflows/update_guides.yml
@@ -0,0 +1,41 @@
+
+name: Update guides
+
+on:
+  push:
+  pull_request:
+    branches: [ main, master ]
+  workflow_dispatch:
+
+jobs:
+
+  update_guides:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: setup python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.8.16'
+
+      - name: install python packages
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: execute table conversion script
+        run: python scripts/guides_table_conversion.py
+
+      - name: Commit if updated
+        run: |
+          git config --local user.email "action@github.com"
+          git config --local user.name "GitHub Action"
+          git add -A
+          git diff-index --quiet HEAD || git commit -m "update guides"
+
+      - name: Push if changes
+        uses: ad-m/github-push-action@v0.6.0
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          branch: main

From 443570cc7c53d366ff854538b787ec7f298a045d Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <johan@biocommons.org.au>
Date: Wed, 17 Apr 2024 14:40:00 +0930
Subject: [PATCH 07/15] Update guides_table_conversion.py

---
 scripts/guides_table_conversion.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/scripts/guides_table_conversion.py b/scripts/guides_table_conversion.py
index 0681e4c..9dc76bb 100644
--- a/scripts/guides_table_conversion.py
+++ b/scripts/guides_table_conversion.py
@@ -21,12 +21,12 @@
 print(f"----> Converting GoogleSheets table to {output_path} started.")
 resource_table = pd.read_csv(url, dtype={'name': str, 'url': str, 'description': str, 'id': str, 'fairsharing': str,
                                          'biotools': str, 'tess': str, 'wfh-collection': str, 'wfh': str,
-                                         'doi': str, 'template': str, 'categories': str})
+                                         'doi': str, 'template': str, 'related_pages': str})
 resource_list = resource_table.to_dict("records")
 clean_resource_list = []
 for resource in resource_list:
-    if not pd.isna(resource['categories']):
-        category_list = resource['categories'].rsplit(sep=",")
+    if not pd.isna(resource['related_pages']):
+        category_list = resource['related_pages'].rsplit(sep=",")
     else:
         category_list = ""
     registry_dict = {}
@@ -38,7 +38,7 @@
     clean_resource_list.append(clean_resource)
     clean_resource['registry'] = registry_dict
     if category_list != "":
-        clean_resource['categories'] = category_list
+        clean_resource['related_pages'] = category_list
 
 print(os.getcwd())
 with open(output_path, 'w+') as yaml_file:

From f58ca363a1b6f6d1db7ae91021cd5a07f722a546 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 17 Apr 2024 05:10:33 +0000
Subject: [PATCH 08/15] update guides

---
 _data/tool_and_resource_list.yml | 36 ++++++++++++++++----------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index 49ca841..dc36b14 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -1,6 +1,4 @@
-- categories:
-  - genome assembly
-  description: This How-to-Guide describes the steps required to assemble your genome
+- description: This How-to-Guide describes the steps required to assemble your genome
     on the Galaxy Australia platform, using multiple workflows developed in consultation
     between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia,
     and the Australian BioCommons.
@@ -9,10 +7,10 @@
   registry:
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
-  url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
-- categories:
+  related_pages:
   - genome assembly
-  description: Once a genome has been assembled, it is important to assess the quality
+  url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
+- description: Once a genome has been assembled, it is important to assess the quality
     of the assembly, and in the first instance, this quality control (QC) can be achieved
     using the workflow described here.
   id: genome-assembly-qc
@@ -20,30 +18,30 @@
   registry:
     tess: genome assembly
     wfh: https://workflowhub.eu/workflows/403
+  related_pages:
+  - genome assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/assembly_qc
-- categories:
-  - documentation
-  description: This web page describes How-to create new How-to Guide websites using
+- description: This web page describes How-to create new How-to Guide websites using
     a GitHub repository template.
   id: how-to-create-guide
   name: How-to Guide for creating a How-to Guide
   registry:
     doi: https://doi.org/10.5281/zenodo.8210268
     template: https://github.com/AustralianBioCommons/guide-template
-  url: https://australianbiocommons.github.io/how-to-guide-template/
-- categories:
+  related_pages:
   - documentation
-  description: The Australian BioCommons has been working with community bioinformaticians
+  url: https://australianbiocommons.github.io/how-to-guide-template/
+- description: The Australian BioCommons has been working with community bioinformaticians
     and our infrastructure partners to establish a guidelines repository that can
     act as a template for documentation of tools and workflows.
   id: doc-guidelines
   name: How-to use the Australian BioCommons documentation guidelines
   registry:
     template: https://github.com/AustralianBioCommons/doc_guidelines
+  related_pages:
+  - documentation
   url: https://australianbiocommons.github.io/how-to-doc-guidelines/
-- categories:
-  - pop_gen
-  description: This How-to Guide describes the steps required to run the Stacks workflows
+- description: This How-to Guide describes the steps required to run the Stacks workflows
     on Galaxy Australia to analyse RADseq data, using workflows developed in consultations
     between the Bioplatforms Australia Threatened Species Initiative, Galaxy Australia,
     and the Australian BioCommons.
@@ -52,13 +50,15 @@
   registry:
     biotools: stacks
     tess: RAD seq
+  related_pages:
+  - pop_gen
   url: https://australianbiocommons.github.io/how-to-guides/stacks_workflows/stacks
-- categories:
-  - metagenomics
-  description: This How-to Guide describes how to use the shotgun metagenomics workflow
+- description: This How-to Guide describes how to use the shotgun metagenomics workflow
     with MetaPhlAn2 on Galaxy Australia. The workflow is using the tools MetaPhlAn2
     for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes.
   id: shotgun-metagenomics-metaphlanv2
   name: Shotgun metagenomics workflow with MetaPhlAn2 on Galaxy Australia
   registry: {}
+  related_pages:
+  - metagenomics
   url: https://vmurigneu.github.io/shotgun_howto_ga_workflows/shotgun_wf_guide

From b730ec0b33899d6482f5da6303c662b86bd42b5d Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <50811354+supernord@users.noreply.github.com>
Date: Thu, 18 Apr 2024 09:14:02 +0930
Subject: [PATCH 09/15] Update tool_and_resource_list.yml

---
 _data/tool_and_resource_list.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index dc36b14..916700d 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -8,7 +8,7 @@
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
   related_pages:
-  - genome assembly
+   - genome assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
 - description: Once a genome has been assembled, it is important to assess the quality
     of the assembly, and in the first instance, this quality control (QC) can be achieved

From 5ffde66d222183ee44f89f1c5de3899556e8076e Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 17 Apr 2024 23:44:34 +0000
Subject: [PATCH 10/15] update guides

---
 _data/tool_and_resource_list.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index 916700d..dc36b14 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -8,7 +8,7 @@
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
   related_pages:
-   - genome assembly
+  - genome assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
 - description: Once a genome has been assembled, it is important to assess the quality
     of the assembly, and in the first instance, this quality control (QC) can be achieved

From 664a10b5b2aba26d75ce89e3c499dc4b1b7709f1 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <50811354+supernord@users.noreply.github.com>
Date: Thu, 18 Apr 2024 09:14:57 +0930
Subject: [PATCH 11/15] Update update_guides.yml

---
 .github/workflows/update_guides.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/update_guides.yml b/.github/workflows/update_guides.yml
index 44bbb13..f6dbd7c 100644
--- a/.github/workflows/update_guides.yml
+++ b/.github/workflows/update_guides.yml
@@ -2,9 +2,6 @@
 name: Update guides
 
 on:
-  push:
-  pull_request:
-    branches: [ main, master ]
   workflow_dispatch:
 
 jobs:

From f617e7f510432c16db475a026dc4c4c6f85880b9 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <50811354+supernord@users.noreply.github.com>
Date: Thu, 18 Apr 2024 09:15:36 +0930
Subject: [PATCH 12/15] Update tool_and_resource_list.yml

---
 _data/tool_and_resource_list.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index dc36b14..916700d 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -8,7 +8,7 @@
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
   related_pages:
-  - genome assembly
+   - genome assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
 - description: Once a genome has been assembled, it is important to assess the quality
     of the assembly, and in the first instance, this quality control (QC) can be achieved

From bfa49c871887112bd35aa5f901ba06ce08317dc6 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <50811354+supernord@users.noreply.github.com>
Date: Thu, 18 Apr 2024 09:18:54 +0930
Subject: [PATCH 13/15] Update tool_and_resource_list.yml

---
 _data/tool_and_resource_list.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index 916700d..dc36b14 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -8,7 +8,7 @@
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
   related_pages:
-   - genome assembly
+  - genome assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
 - description: Once a genome has been assembled, it is important to assess the quality
     of the assembly, and in the first instance, this quality control (QC) can be achieved

From 6450b1f914a59bd6a7749be1490a32a0cc6649a8 Mon Sep 17 00:00:00 2001
From: GitHub Action <action@github.com>
Date: Wed, 17 Apr 2024 23:52:57 +0000
Subject: [PATCH 14/15] update guides

---
 _data/tool_and_resource_list.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/_data/tool_and_resource_list.yml b/_data/tool_and_resource_list.yml
index dc36b14..5cea358 100644
--- a/_data/tool_and_resource_list.yml
+++ b/_data/tool_and_resource_list.yml
@@ -8,7 +8,7 @@
     tess: genome assembly
     wfh-collection: https://workflowhub.eu/collections/5
   related_pages:
-  - genome assembly
+  - genome_assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/hifi_assembly
 - description: Once a genome has been assembled, it is important to assess the quality
     of the assembly, and in the first instance, this quality control (QC) can be achieved
@@ -19,7 +19,7 @@
     tess: genome assembly
     wfh: https://workflowhub.eu/workflows/403
   related_pages:
-  - genome assembly
+  - genome_assembly
   url: https://australianbiocommons.github.io/how-to-guides/genome_assembly/assembly_qc
 - description: This web page describes How-to create new How-to Guide websites using
     a GitHub repository template.

From c7d2275c768472a2b520d1af33128ad6f7357835 Mon Sep 17 00:00:00 2001
From: Johan Gustafsson <johan@biocommons.org.au>
Date: Thu, 18 Apr 2024 09:27:41 +0930
Subject: [PATCH 15/15] Add metagenomics.md

---
 pages/metagenomics.md | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 pages/metagenomics.md

diff --git a/pages/metagenomics.md b/pages/metagenomics.md
new file mode 100644
index 0000000..40f1547
--- /dev/null
+++ b/pages/metagenomics.md
@@ -0,0 +1,9 @@
+---
+title: Metagenomics
+type: category
+page_id: metagenomics
+description: How-to Guides focused on metagenomics.
+---
+
+
+