Bump versions of metaphlan, humann, and update CHANGELOG

CHANGELOG.md

@@ -20,7 +20,10 @@ situations.
   broken in the later versions of Snakemake.
 - Add KrakenUniq as taxonomic profiler as an alternative with lower false
   positive rate than Kraken2.
-- Added samplesheet as alternative input file selection method.
+- Added samplesheet as alternative input file selection method, this also
+  enables providing custom sample names that are not based on pattern in input
+  filenames.
+- Samplesheet can be used to specify remote input files from S3 or HTTP/HTTPS sources.
 - Added `run_krona` setting for taxonomic profilers to make it possible to disable Krona
   table and plot creation.
 
@@ -34,7 +37,8 @@ situations.
 
 ### Changed
 - Replaced CircleCI automatic testing workflow with one implemented with Github actions.
-- Updated MetaPhlAn to version 4.0.0.
+- Updated MetaPhlAn to version 4.0.3.
+- Updated HUMAnN to version 3.6.
 - Modified area and MetaPhlAn heatmap plotting scripts to better deal
   with MetaPhlAn 4 output formats.
 - Updated the documentation to reflect recent changes in StaG.

envs/Singularity.biobakery

@@ -11,7 +11,7 @@ From: mambaorg/micromamba:0.17.0
 		-c bioconda \
 		-c conda-forge \
 		-c biobakery \
-		python=3.7 metaphlan=4.0.2 humann=3.5 krona=2.8.1
+		python=3.7 metaphlan=4.0.3 humann=3.6 krona=2.8.1
 	micromamba clean --yes --all
 
 	humann_databases --download utility_mapping full /opt/humann --update-config yes

envs/humann.yaml

@@ -5,4 +5,4 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - humann=3.5
+    - humann=3.6

envs/metaphlan.yaml

@@ -5,5 +5,5 @@ channels:
     - defaults
     - biobakery
 dependencies:
-    - metaphlan =4.0.2
+    - metaphlan =4.0.3
     - krona =2.8.1