Bring dev in sync with master

.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/source/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

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