From dccafde3dd0af2872302ba46a3774116c5d4a726 Mon Sep 17 00:00:00 2001
From: Fredrik Boulund <boulund@users.noreply.github.com>
Date: Fri, 17 Nov 2023 14:42:51 +0100
Subject: [PATCH 1/3] Create .readthedocs.yaml

---
 .readthedocs.yaml | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)
 create mode 100644 .readthedocs.yaml

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
new file mode 100644
index 0000000..f3aa1f5
--- /dev/null
+++ b/.readthedocs.yaml
@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#   - requirements: docs/requirements.txt

From f38835800c46ff5400a71de9611e24f49c057556 Mon Sep 17 00:00:00 2001
From: Fredrik Boulund <boulund@users.noreply.github.com>
Date: Fri, 17 Nov 2023 14:58:15 +0100
Subject: [PATCH 2/3] Update .readthedocs.yaml

---
 .readthedocs.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index f3aa1f5..0ff5596 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -13,7 +13,7 @@ build:
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: docs/conf.py
+  configuration: docs/source/conf.py
 
 # We recommend specifying your dependencies to enable reproducible builds:
 # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html

From 2949f1eb9d9e97608a89b48de66f863d4409fe3b Mon Sep 17 00:00:00 2001
From: Fredrik Boulund <boulund@users.noreply.github.com>
Date: Wed, 17 Jan 2024 08:04:55 +0100
Subject: [PATCH 3/3] Fix broken kraken2/bowtie2 host removal resources
 settings

---
 profiles/ctmr_gandalf/config.yaml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/profiles/ctmr_gandalf/config.yaml b/profiles/ctmr_gandalf/config.yaml
index 0536a00..62744f4 100644
--- a/profiles/ctmr_gandalf/config.yaml
+++ b/profiles/ctmr_gandalf/config.yaml
@@ -49,8 +49,8 @@ default-resources:
   - mem_mb=10240
 set-threads:
   - fastp=20
-  - kraken2_remove_host=20
-  - bowtie2_remove_host=20
+  - kraken2_host_removal=20
+  - bowtie2_host_removal=20
   - bbcountunique=4
   - sketch=8
   - kaiju=32
@@ -70,10 +70,10 @@ set-threads:
 set-resources:
   - fastp:mem_mb=20240
   - fastp:time="02:00:00"
-  - kraken2_remove_host:mem_mb=10240
-  - kraken2_remove_host:time="02:00:00"
-  - bowtie2_remove_host:mem_mb=10240
-  - bowtie2_remove_host:time="06:00:00"
+  - kraken2_host_removal:mem_mb=10240
+  - kraken2_host_removal:time="02:00:00"
+  - bowtie2_host_removal:mem_mb=10240
+  - bowtie2_host_removal:time="06:00:00"
   - kaiju:mem_mb=10240
   - kaiju:time="10:00:00"
   - kraken2:mem_mb=10240