diff --git a/CHANGELOG.md b/CHANGELOG.md
index f4a16aa..815c757 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -15,14 +15,28 @@ situations.
 
 ## [0.7.1] Unreleased
 ### Added
+- Slurm profile for PDC Dardel. Uses Snakemake's grouping feature to group
+  multiple HUMAnN jobs together on high memory nodes to better optimize core
+  billing for high-memory jobs such as HUMAnN.
 
 ### Fixed
+- Slurm profile: Fixed the incorrect rule names used for allocations for host
+  removal steps.
 
 ### Changed
+- Moved container specifications into config file. Now using more detailed
+  container specifications for most rules. This also enables easier use of
+  local copies of containers (e.g. in HPC environments without external network
+  access).
+- Changed compression of kraken2 host removal artifacts to use gzip instead of
+  pigz due to the latter not being present in the kraken2 biocontainer.
+- HUMANnN3: Updated to version 3.9, compatible with MetaPhlAn4 vJun23 database.
   
 ### Deprecated
 
 ### Removed
+- Removed mentions of assembly workflow from docs and config.
+- Removed outdated amrplusplus scripts left behind in the scripts subdirectory.
 
 
 ## [0.7.0] 2023-06-13
diff --git a/config/config.yaml b/config/config.yaml
index ba9a8ce..b7e1ab4 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -17,7 +17,6 @@ input_fn_pattern: "{sample}_{readpair}.fq.gz"
 samplesheet: ""           # Three-column samplesheet with sample_id,fastq_1,fastq_2 columns. Used instead of inputdir
 outdir: "output_dir"
 logdir: "output_dir/logs"
-dbdir: "databases"        # Databases will be downloaded to this dir
 report: "StaG_report-"    # Filename prefix for report file ("-{datetime}.html" automatically appended)
 email: ""                 # Email to send status message after completed/failed run.
 
@@ -29,6 +28,25 @@ s3_endpoint_url: "https://s3.ki.se"  # Use https://s3.amazonaws.com for Amazon S
 keep_local: False                    # Keep local copies of remote input files, default False.
 
 
+#########################
+# Container images
+#########################
+containers:
+    bbmap: "docker://quay.io/biocontainers/bbmap:39.06--h92535d8_0"
+    bowtie2: "docker://quay.io/biocontainers/bowtie2:2.5.1--py38he00c5e5_2"
+    bracken: "docker://quay.io/biocontainers/bracken:2.9--py39h1f90b4d_0"
+    fastp: "docker://quay.io/biocontainers/fastp:0.23.4--hadf994f_2"
+    humann: "docker://quay.io/biocontainers/humann:3.9--py312hdfd78af_0"
+    kaiju: "docker://quai.io/biocontainers/kaiju:1.10.1--h43eeafb_0"
+    kraken2: "docker://quay.io/biocontainers/kraken2:2.1.3--pl5321hdcf5f25_0"
+    krakenuniq: "docker://quay.io/biocontainers/krakenuniq:1.0.4--pl5321h6dccd9a_1"
+    krona: "docker://quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1"
+    metaphlan: "docker://quay.io/biocontainers/metaphlan:4.1.0--pyhca03a8a_0"
+    multiqc: "docker://quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
+    samtools: "docker://quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
+    stag: "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc-develop"
+
+
 #########################
 # Pipeline steps included
 #########################
@@ -52,8 +70,6 @@ functional_profile:
 mappers:
     bbmap: False
     bowtie2: False
-assembly: False
-binning: False
 
 
 #########################
@@ -190,8 +206,3 @@ bowtie2:
           attribute_type: ""   # Attribute type to summarize counts for, default is "gene_id" (any attribute in the GTF file's attribute field can be used)
           extra: ""            # Extra featureCount command line parameters
 
-
-#########################
-# Assembly
-#########################
-# Assembly workflow was removed in StaG v0.7.0
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 8ae3efe..0785d06 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -56,9 +56,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.7.0'
+version = '0.7.1'
 # The full version, including alpha/beta/rc tags.
-release = '0.7.0'
+release = '0.7.1-dev'
 
 # reStructuredText prolog contains a string of reStructuredText that will be
 # included at the beginning of every source file that is read.
diff --git a/docs/source/overview.rst b/docs/source/overview.rst
index d638c8f..78cdf4e 100644
--- a/docs/source/overview.rst
+++ b/docs/source/overview.rst
@@ -15,6 +15,3 @@ The following image shows a simplified graph of the workflow of |full_name|:
     :alt: StaG mwc
     :align: left
 
-Note that several parts of the workflow are not yet implemented, most notably
-the structure of the sections performing metagenomic assembly are not yet
-finalized.
diff --git a/profiles/ctmr_gandalf/config.yaml b/profiles/ctmr_gandalf/config.yaml
index 0536a00..bca0d26 100644
--- a/profiles/ctmr_gandalf/config.yaml
+++ b/profiles/ctmr_gandalf/config.yaml
@@ -48,9 +48,9 @@ default-resources:
   - time="01:00:00"
   - mem_mb=10240
 set-threads:
-  - fastp=20
-  - kraken2_remove_host=20
-  - bowtie2_remove_host=20
+  - fastp=16
+  - 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="03:00:00"
+  - bowtie2_host_removal:mem_mb=10240
+  - bowtie2_host_removal:time="08:00:00"
   - kaiju:mem_mb=10240
   - kaiju:time="10:00:00"
   - kraken2:mem_mb=10240
diff --git a/profiles/pdc_dardel/config.yaml b/profiles/pdc_dardel/config.yaml
new file mode 100644
index 0000000..2fb9ee7
--- /dev/null
+++ b/profiles/pdc_dardel/config.yaml
@@ -0,0 +1,101 @@
+# Snakemake profile for StaG for use on PDC Dardel
+# Fredrik Boulund 2024
+
+#######################################
+# General Snakemake settings
+#######################################
+configfile: config/config.yaml
+keep-going: False
+rerun-incomplete: True
+printshellcmds: True
+scheduler: greedy
+conda-frontend: conda
+use-conda: True
+conda-prefix: /cfs/klemming/projects/supr/naiss2023-6-372/sing/smk_conda_envs
+#use-singularity: True
+#singularity-prefix: /cfs/klemming/projects/supr/naiss2023-6-372/sing
+#singularity-args: "-B /cfs/klemming/projects/supr/naiss2023-6-372/"
+groups: humann=group0
+group-components: group0=4
+
+#######################################
+# Cluster settings
+#######################################
+cluster:
+  mkdir -p slurm_logs/{rule} &&
+  sbatch
+    --account={resources.account}
+    --partition={resources.partition}
+    --nodes=1
+    --ntasks-per-node=1
+    --cpus-per-task={threads}
+    --mem={resources.mem_mb}
+    --time={resources.time}
+    --job-name={rule}-{wildcards}
+    --output=slurm_logs/{rule}/{rule}-{wildcards}-%j.out
+    --parsable
+cluster-cancel: scancel
+cluster-cancel-nargs: 50
+cluster-status: status-sacct.sh
+restart-times: 0
+max-jobs-per-second: 10
+max-status-checks-per-second: 1
+latency-wait: 60
+jobs: 500
+
+#######################################
+# Resource settings
+#######################################
+local-cores: 2
+default-resources:
+  - threads=2
+  - account=naiss2023-5-552
+  - partition=shared
+  - time="01:00:00"
+  - mem_mb="1G"
+set-threads:
+  - fastp=10
+  - kraken2_host_removal=20
+  - bowtie2_host_removal=10
+  - bt2_sort_bam_files=4
+  - bbcountunique=4
+  - sketch=8
+  - kaiju=32
+  - kraken2=16
+  - krakenuniq=24
+  - metaphlan=12
+  - strainphlan=8
+  - bracken=2
+  - humann=30
+  - bbmap=16
+  - bowtie2=16
+  - assembly=20
+  - consolidate_bins=20
+  - blobology=20
+set-resources:
+  - fastp:mem_mb=4G
+  - fastp:time=02:00:00
+  - kraken2_host_removal:mem_mb=8G
+  - kraken2_host_removal:time=02:00:00
+  - bowtie2_host_removal:mem_mb=8G
+  - bowtie2_host_removal:time=06:00:00
+  - bt2_sort_bam_files:mem_mb=30G
+  - bt2_sort_bam_files:time=01:00:00
+  - kaiju:mem_mb=8G
+  - kaiju:time=10:00:00
+  - kraken2:mem_mb=160G
+  - kraken2:time=04:00:00
+  - krakenuniq:mem_mb=100G
+  - krakenuniq:time=06:00:00
+  - metaphlan:mem_mb=30G
+  - metaphlan:time=04:00:00
+  - strainphlan:mem_mb=10G
+  - strainphlan:time=02:00:00
+  - humann:partition=memory
+  - humann:mem_mb=850G
+  - humann:time=23:00:00
+  - humann:tmpdir=/cfs/klemming/scratch/b/boulund/
+  - bbmap:mem_mb=16G
+  - bbmap:time=04:00:00
+  - bowtie2:mem_mb=16G
+  - bowtie2:time=04:00:00
diff --git a/profiles/pdc_dardel/status-sacct.sh b/profiles/pdc_dardel/status-sacct.sh
new file mode 100755
index 0000000..53752f5
--- /dev/null
+++ b/profiles/pdc_dardel/status-sacct.sh
@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+# Check status of Slurm job
+
+jobid="$1"
+
+if [[ "$jobid" == Submitted ]]
+then
+  echo smk-simple-slurm: Invalid job ID: "$jobid" >&2
+  echo smk-simple-slurm: Did you remember to add the flag --parsable to your sbatch call? >&2
+  exit 1
+fi
+
+output=`sacct -j "$jobid" --format State --noheader | head -n 1 | awk '{print $1}'`
+
+if [[ $output =~ ^(COMPLETED).* ]]
+then
+  echo success
+elif [[ $output =~ ^(RUNNING|PENDING|COMPLETING|CONFIGURING|SUSPENDED).* ]]
+then
+  echo running
+else
+  echo failed
+fi
diff --git a/workflow/Snakefile b/workflow/Snakefile
index 7856dea..72adf80 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -21,8 +21,7 @@ from scripts.common import UserMessages, SampleSheet
 
 user_messages = UserMessages()
 
-stag_version = "0.7.0"
-singularity_branch_tag = "-master"  # Replace with "-master" before publishing new version
+stag_version = "0.7.1"
 
 configfile: "config/config.yaml"
 report: "report/workflow.rst"
@@ -31,17 +30,20 @@ citations = {publications["StaG"], publications["Snakemake"]}
 INPUTDIR = Path(config["inputdir"])
 OUTDIR = Path(config["outdir"])
 LOGDIR = Path(config["logdir"])
-DBDIR = Path(config["dbdir"])
 all_outputs = []
 
 if config["samplesheet"]:
-    samplesheet = SampleSheet(config["samplesheet"], keep_local=config["keep_local"], endpoint_url=config["s3_endpoint_url"])
+    samplesheet = SampleSheet(
+            samplesheet=config["samplesheet"],
+            keep_local=config["keep_local"],
+            endpoint_url=config["s3_endpoint_url"],
+    )
     SAMPLES = samplesheet.samples
     INPUT_read1 = lambda w: samplesheet.sample_info[w.sample]["read1"]
     INPUT_read2 = lambda w: samplesheet.sample_info[w.sample]["read2"]
 else:
     SAMPLES = set(glob_wildcards(INPUTDIR/config["input_fn_pattern"]).sample)
-    INPUT_read1 = INPUTDIR/config["input_fn_pattern"].format(sample="{sample}", readpair="1"),
+    INPUT_read1 = INPUTDIR/config["input_fn_pattern"].format(sample="{sample}", readpair="1")
     INPUT_read2 = INPUTDIR/config["input_fn_pattern"].format(sample="{sample}", readpair="2")
 
 onstart:
@@ -60,7 +62,8 @@ onstart:
         if config["samplesheet"]:
             print(f"Found these samples in '{config['samplesheet']}':\n{SAMPLES}")
         else:
-            print(f"Found these samples in '{config['inputdir']}' using input filename pattern '{config['input_fn_pattern']}':\n{SAMPLES}")
+            print(f"Found these samples in '{config['inputdir']}' using "
+                   "input filename pattern '{config['input_fn_pattern']}':\n{SAMPLES}")
 
 
 #############################
@@ -100,10 +103,6 @@ include: "rules/functional_profiling/humann.smk"
 include: "rules/mappers/bbmap.smk"
 include: "rules/mappers/bowtie2.smk"
 
-#############################
-# Assembly
-#############################
-
 #############################
 # MultiQC
 #############################
diff --git a/workflow/envs/humann.yaml b/workflow/envs/humann.yaml
index cb7d6a8..febe011 100644
--- a/workflow/envs/humann.yaml
+++ b/workflow/envs/humann.yaml
@@ -5,4 +5,4 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - humann=3.7
+    - humann=3.9
diff --git a/workflow/envs/krakenuniq.yaml b/workflow/envs/krakenuniq.yaml
index 3a1248a..2323b42 100644
--- a/workflow/envs/krakenuniq.yaml
+++ b/workflow/envs/krakenuniq.yaml
@@ -4,4 +4,4 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - krakenuniq =1.0.3
+    - krakenuniq =1.0.4
diff --git a/workflow/envs/metaphlan.yaml b/workflow/envs/metaphlan.yaml
index 647e3e6..5e459c4 100644
--- a/workflow/envs/metaphlan.yaml
+++ b/workflow/envs/metaphlan.yaml
@@ -4,5 +4,5 @@ channels:
     - bioconda
     - defaults
 dependencies:
-    - metaphlan =4.0.6
+    - metaphlan =4.1.0
     - krona =2.8.1
diff --git a/workflow/envs/stag-mwc.yaml b/workflow/envs/stag-mwc.yaml
index c7aed39..3890f2b 100644
--- a/workflow/envs/stag-mwc.yaml
+++ b/workflow/envs/stag-mwc.yaml
@@ -5,21 +5,20 @@ channels:
     - defaults
 dependencies:
     - python =3.10.9
-    - fastp =0.23.2
-    - bbmap =39.01
-    - kaiju =1.9.2
-    - kraken2 =2.1.2
-    - bracken =2.8
+    - bbmap =39.06
+    - bracken =2.9
+    - fastp =0.23.4
+    - kaiju =1.10.1
+    - kraken2 =2.1.3
     - krona =2.8.1
     - matplotlib =3.7.1
-    - multiqc =1.14
+    - multiqc =1.21
     - pandas =2.0.0
+    - pigz =2.6
+    - sambamba =1.0
+    - samtools =1.19.2
     - seaborn =0.12.2
     - subread =2.0.3
-    - sambamba =1.0
-    - samtools =1.6
-    - groot =1.1.2
-    - pigz =2.6
     - pip
     - pip:
         - fastcluster
diff --git a/workflow/rules/functional_profiling/humann.smk b/workflow/rules/functional_profiling/humann.smk
index 3887659..3d7bdc4 100644
--- a/workflow/rules/functional_profiling/humann.smk
+++ b/workflow/rules/functional_profiling/humann.smk
@@ -48,7 +48,7 @@ rule humann:
     conda:
         "../../envs/humann.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["humann"]
     threads: 20
     params:
         outdir=f"{OUTDIR}/humann/",
@@ -96,7 +96,7 @@ rule normalize_humann_tables:
     conda:
         "../../envs/humann.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["humann"]
     threads: 1
     params:
         method=h_config["norm_method"],
@@ -143,7 +143,7 @@ rule humann_join_tables:
     conda:
         "../../envs/humann.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["humann"]
     threads: 
         1
     params:
@@ -174,3 +174,4 @@ rule humann_join_tables:
             >> {log.stdout} \
             2>> {log.stderr}
         """
+
diff --git a/workflow/rules/mappers/bbmap.smk b/workflow/rules/mappers/bbmap.smk
index 29361bd..a270b6c 100644
--- a/workflow/rules/mappers/bbmap.smk
+++ b/workflow/rules/mappers/bbmap.smk
@@ -1,6 +1,5 @@
 # vim: syntax=python expandtab
 # Rules for generic read mapping using BBMap
-# TODO: Remove superfluous str conversions when Snakemake is pathlib compatible.
 from pathlib import Path
 
 from snakemake.exceptions import WorkflowError
@@ -20,14 +19,14 @@ for bbmap_config in config["bbmap"]:
 
         # Add final output files from this module to 'all_outputs' from the main
         # Snakefile scope. SAMPLES is also from the main Snakefile scope.
-        bbmap_alignments = expand(str(OUTDIR/"bbmap/{db_name}/{sample}.{output_type}"),
+        bbmap_alignments = expand(OUTDIR/"bbmap/{db_name}/{sample}.{output_type}",
                 db_name=db_name,
                 sample=SAMPLES,
                 output_type=("bam", "covstats.txt", "rpkm.txt"))
-        counts_table = expand(str(OUTDIR/"bbmap/{db_name}/counts.{column}.tsv"),
+        counts_table = expand(OUTDIR/"bbmap/{db_name}/counts.{column}.tsv",
                 db_name=db_name,
                 column=map(str.strip, bbmap_config["counts_table"]["columns"].split(",")))
-        featureCounts = expand(str(OUTDIR/"bbmap/{db_name}/all_samples.featureCounts{output_type}"),
+        featureCounts = expand(OUTDIR/"bbmap/{db_name}/all_samples.featureCounts{output_type}",
                 db_name=db_name,
                 sample=SAMPLES,
                 output_type=["", ".summary", ".table.txt"])
@@ -64,8 +63,8 @@ for bbmap_config in config["bbmap"]:
             bamscript=temp(bbmap_output_folder/"{sample}.bamscript.sh"),
             bamfile=bbmap_output_folder/"{sample}.bam" if bbmap_config["keep_bam"] else temp(bbmap_output_folder/"{sample}.bam"),
         log:
-            stdout=str(bbmap_logdir/"{sample}.bbmap.stdout.log"),
-            stderr=str(bbmap_logdir/"{sample}.bbmap.statsfile.txt"),
+            stdout=bbmap_logdir/"{sample}.bbmap.stdout.log",
+            stderr=bbmap_logdir/"{sample}.bbmap.statsfile.txt",
         message:
             "Mapping {{wildcards.sample}} to {db_name} using BBMap".format(db_name=db_name)
         shadow:
@@ -73,7 +72,7 @@ for bbmap_config in config["bbmap"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["bbmap"]
         threads: 8
         params:
             db_path=bbmap_config["db_path"],
@@ -108,16 +107,16 @@ for bbmap_config in config["bbmap"]:
         f"""Summarize read counts for {db_name}"""
         name: f"bbmap_counts_{db_name}"
         input:
-            rpkms=expand(str(OUTDIR/"bbmap/{db_name}/{sample}.rpkm.txt"),
+            rpkms=expand(OUTDIR/"bbmap/{db_name}/{sample}.rpkm.txt",
                     db_name=db_name,
                     sample=SAMPLES)
         output:
-            expand(str(OUTDIR/"bbmap/{db_name}/counts.{column}.tsv"),
+            expand(OUTDIR/"bbmap/{db_name}/counts.{column}.tsv",
                     db_name=db_name,
                     column=map(str.strip, bbmap_config["counts_table"]["columns"].split(","))
             )
         log:
-            str(bbmap_logdir/"counts.log")
+            bbmap_logdir/"counts.log"
         message:
             "Summarizing read counts for {db_name}".format(db_name=db_name)
         shadow:
@@ -125,7 +124,7 @@ for bbmap_config in config["bbmap"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["stag"]
         threads: 1
         params:
             annotations=bbmap_config["counts_table"]["annotations"],
@@ -147,7 +146,7 @@ for bbmap_config in config["bbmap"]:
         f"""Summarize feature counts for {db_name}"""
         name: f"bbmap_feature_counts_{db_name}"
         input:
-            bams=expand(str(OUTDIR/"bbmap/{db_name}/{sample}.bam"),
+            bams=expand(OUTDIR/"bbmap/{db_name}/{sample}.bam",
                     db_name=db_name,
                     sample=SAMPLES)
         output:
@@ -155,7 +154,7 @@ for bbmap_config in config["bbmap"]:
             counts_table=OUTDIR/"bbmap/{db_name}/all_samples.featureCounts.table.txt".format(db_name=db_name),
             summary=OUTDIR/"bbmap/{db_name}/all_samples.featureCounts.summary".format(db_name=db_name),
         log:
-            str(bbmap_logdir/"all_samples.featureCounts.log")
+            bbmap_logdir/"all_samples.featureCounts.log"
         message:
             "Summarizing feature counts for {db_name}".format(db_name=db_name)
         shadow:
@@ -163,7 +162,7 @@ for bbmap_config in config["bbmap"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["stag"]
         threads: 4
         params:
             annotations=fc_config["annotations"],
@@ -183,6 +182,7 @@ for bbmap_config in config["bbmap"]:
                 {input.bams} \
                 > {log} \
                 2>> {log}
+
             cut \
                 -f1,7- \
                 {output.counts}  \
diff --git a/workflow/rules/mappers/bowtie2.smk b/workflow/rules/mappers/bowtie2.smk
index 3b19c62..2d5b0d3 100644
--- a/workflow/rules/mappers/bowtie2.smk
+++ b/workflow/rules/mappers/bowtie2.smk
@@ -1,6 +1,5 @@
 # vim: syntax=python expandtab
 # Generic rules for alignment of reads to a reference database using Bowtie2
-# TODO: Remove superfluous str conversions when Snakemake is pathlib compatible.
 from pathlib import Path
 
 from snakemake.exceptions import WorkflowError
@@ -17,17 +16,17 @@ for bt2_config in config["bowtie2"]:
 
         # Add final output files from this module to 'all_outputs' from the main
         # Snakefile scope. SAMPLES is also from the main Snakefile scope.
-        bowtie2_alignments = expand(str(OUTDIR/"bowtie2/{db_name}/{sample}.bam"),
+        bowtie2_alignments = expand(OUTDIR/"bowtie2/{db_name}/{sample}.bam",
                 sample=SAMPLES,
                 db_name=bt2_db_name)
-        bowtie2_stats = expand(str(OUTDIR/"bowtie2/{db_name}/{sample}.{stats}.txt"),
+        bowtie2_stats = expand(OUTDIR/"bowtie2/{db_name}/{sample}.{stats}.txt",
                 sample=SAMPLES,
                 stats=["covstats", "rpkm"],
                 db_name=bt2_db_name)
-        counts_table = expand(str(OUTDIR/"bowtie2/{db_name}/counts.{column}.tsv"),
+        counts_table = expand(OUTDIR/"bowtie2/{db_name}/counts.{column}.tsv",
                 db_name=bt2_db_name,
                 column=map(str.strip, bt2_config["counts_table"]["columns"].split(",")))
-        featureCounts = expand(str(OUTDIR/"bowtie2/{db_name}/all_samples.featureCounts{output_type}"),
+        featureCounts = expand(OUTDIR/"bowtie2/{db_name}/all_samples.featureCounts{output_type}",
                 db_name=bt2_db_name,
                 sample=SAMPLES,
                 output_type=["", ".summary", ".table.txt"])
@@ -61,7 +60,7 @@ for bt2_config in config["bowtie2"]:
         output:
             OUTDIR/"bowtie2/{db_name}/{{sample}}.bam".format(db_name=bt2_db_name) if bt2_config["keep_bam"] else temp(OUTDIR/"bowtie2/{db_name}/{{sample}}.bam".format(db_name=bt2_db_name)),
         log:
-            str(LOGDIR/"bowtie2/{db_name}/{{sample}}.log".format(db_name=bt2_db_name))
+            LOGDIR/"bowtie2/{db_name}/{{sample}}.log".format(db_name=bt2_db_name)
         message:
             "Mapping {{wildcards.sample}} to {db_name} using Bowtie2".format(db_name=bt2_db_name)
         params:
@@ -71,7 +70,7 @@ for bt2_config in config["bowtie2"]:
         conda:
             "../../envs/metaphlan.yaml"
         container:
-            "docker://quay.io/biocontainers/metaphlan:4.0.3--pyhca03a8a_0"
+            config["containers"]["bowtie2"]
         wrapper:
             "0.23.1/bio/bowtie2/align"
 
@@ -85,7 +84,7 @@ for bt2_config in config["bowtie2"]:
             covstats=OUTDIR/"bowtie2/{db_name}/{{sample}}.covstats.txt".format(db_name=bt2_db_name),
             rpkm=OUTDIR/"bowtie2/{db_name}/{{sample}}.rpkm.txt".format(db_name=bt2_db_name)
         log:
-            str(LOGDIR/"bowtie2/{db_name}/{{sample}}.pileup.log".format(db_name=bt2_db_name))
+            LOGDIR/"bowtie2/{db_name}/{{sample}}.pileup.log".format(db_name=bt2_db_name)
         message:
             "Summarizing bowtie2 mapping statistics against {db_name}.".format(db_name=bt2_db_name)
         shadow:
@@ -93,7 +92,7 @@ for bt2_config in config["bowtie2"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["bbmap"]
         shell:
             """
             pileup.sh \
@@ -112,16 +111,16 @@ for bt2_config in config["bowtie2"]:
         """Create count table for Bowtie2 mappings."""
         name: f"bowtie2_count_table_{bt2_db_name}"
         input:
-            rpkms=expand(str(OUTDIR/"bowtie2/{db_name}/{sample}.rpkm.txt"),
+            rpkms=expand(OUTDIR/"bowtie2/{db_name}/{sample}.rpkm.txt",
                     db_name=bt2_db_name,
                     sample=SAMPLES)
         output:
-            expand(str(OUTDIR/"bowtie2/{db_name}/counts.{column}.tsv"),
+            expand(OUTDIR/"bowtie2/{db_name}/counts.{column}.tsv",
                     db_name=bt2_db_name,
                     column=map(str.strip, bt2_config["counts_table"]["columns"].split(","))
             )
         log:
-            str(LOGDIR/"bowtie2/{db_name}/counts.log".format(db_name=bt2_db_name))
+            LOGDIR/"bowtie2/{db_name}/counts.log".format(db_name=bt2_db_name)
         message:
             "Creating count table for mappings to {db_name}".format(db_name=bt2_db_name)
         shadow:
@@ -129,7 +128,7 @@ for bt2_config in config["bowtie2"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["stag"]
         threads: 1
         params:
             annotations=bt2_config["counts_table"]["annotations"],
@@ -151,7 +150,7 @@ for bt2_config in config["bowtie2"]:
         """Summarize featureCounts for Bowtie2 mappings."""
         name: f"bowtie2_feature_counts_{bt2_db_name}"
         input:
-            bams=expand(str(OUTDIR/"bowtie2/{db_name}/{sample}.bam"),
+            bams=expand(OUTDIR/"bowtie2/{db_name}/{sample}.bam",
                     db_name=bt2_db_name,
                     sample=SAMPLES)
         output:
@@ -159,7 +158,7 @@ for bt2_config in config["bowtie2"]:
             counts_table=OUTDIR/"bowtie2/{db_name}/all_samples.featureCounts.table.txt".format(db_name=bt2_db_name),
             summary=OUTDIR/"bowtie2/{db_name}/all_samples.featureCounts.summary".format(db_name=bt2_db_name),
         log:
-            str(LOGDIR/"bowtie2/{db_name}/all_samples.featureCounts.log".format(db_name=bt2_db_name))
+            LOGDIR/"bowtie2/{db_name}/all_samples.featureCounts.log".format(db_name=bt2_db_name)
         message:
             "Summarizing feature counts for {db_name} mappings.".format(db_name=bt2_db_name)
         shadow:
@@ -167,7 +166,7 @@ for bt2_config in config["bowtie2"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["stag"]
         threads: 4
         params:
             annotations=fc_config["annotations"],
@@ -187,7 +186,7 @@ for bt2_config in config["bowtie2"]:
                 {input.bams} \
                 > {log} \
                 2>> {log} \
-            && \
+
             cut \
                 -f1,7- \
                 {output.counts}  \
@@ -195,3 +194,4 @@ for bt2_config in config["bowtie2"]:
                 | sed 's|\t\w\+/bowtie2/{params.dbname}/|\t|g' \
                 > {output.counts_table}
             """
+
diff --git a/workflow/rules/multiqc/multiqc.smk b/workflow/rules/multiqc/multiqc.smk
index 6517092..02cdce6 100644
--- a/workflow/rules/multiqc/multiqc.smk
+++ b/workflow/rules/multiqc/multiqc.smk
@@ -9,17 +9,17 @@ if config["multiqc_report"]:
         input:
             all_outputs
         output:
-            report=report(f"{OUTDIR}/multiqc/multiqc_report.html",
+            report=report(OUTDIR/"multiqc/multiqc_report.html",
                 category="Sequencing data quality",
                 caption="../../report/multiqc.rst"),
         log:
-           f"{LOGDIR}/multiqc/multiqc.log"
+           LOGDIR/"multiqc/multiqc.log"
         shadow:
             "shallow"
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["multiqc"]
         threads: 1
         params:
             extra=mqc_config["extra"],
@@ -32,4 +32,5 @@ if config["multiqc_report"]:
             """
 
     # Appended after the rule definition to avoid circular dependency
-    all_outputs.append(f"{OUTDIR}/multiqc/multiqc_report.html")
+    all_outputs.append(OUTDIR/"multiqc/multiqc_report.html")
+
diff --git a/workflow/rules/naive/bbcountunique.smk b/workflow/rules/naive/bbcountunique.smk
index 963c41b..023ee95 100644
--- a/workflow/rules/naive/bbcountunique.smk
+++ b/workflow/rules/naive/bbcountunique.smk
@@ -1,6 +1,5 @@
 # vim: syntax=python expandtab
 # Assess sequencing depth of sample using BBCountUnique from the BBMap suite.
-# TODO: Remove superfluous str conversions when Snakemake is pathlib compatible.
 
 if config["naive"]["assess_depth"]:
     # Add final output files from this module to 'all_outputs' from
@@ -18,19 +17,16 @@ if config["naive"]["assess_depth"]:
             INPUT_read1,
         output:
             txt=OUTDIR/"bbcountunique/{sample}.bbcountunique.txt",
-            pdf=report(OUTDIR/"bbcountunique/{sample}.bbcountunique.pdf",
-                       caption="../../report/bbcountunique.rst",
-                       category="Sequencing depth")
         log:
-            stdout=str(LOGDIR/"bbcountunique/{sample}.bbcountunique.stdout.log"),
-            stderr=str(LOGDIR/"bbcountunique/{sample}.bbcountunique.stderr.log"),
+            stdout=LOGDIR/"bbcountunique/{sample}.bbcountunique.stdout.log",
+            stderr=LOGDIR/"bbcountunique/{sample}.bbcountunique.stderr.log",
         shadow: 
             "shallow"
         threads: 2
         conda:
             "../../envs/stag-mwc.yaml",
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["bbmap"]
         params:
             interval=config["bbcountunique"]["interval"]
         shell:
@@ -41,9 +37,30 @@ if config["naive"]["assess_depth"]:
               interval={params.interval} \
               > {log.stdout} \
               2> {log.stderr}
+            """
 
+    rule plot_bbcountunique:
+        """Assess sequencing depth using BBCountUnique."""
+        input:
+            txt=OUTDIR/"bbcountunique/{sample}.bbcountunique.txt",
+        output:
+            pdf=report(OUTDIR/"bbcountunique/{sample}.bbcountunique.pdf",
+                       caption="../../report/bbcountunique.rst",
+                       category="Sequencing depth")
+        log:
+            stdout=LOGDIR/"bbcountunique/{sample}.plot_bbcountunique.stdout.log",
+            stderr=LOGDIR/"bbcountunique/{sample}.plot_bbcountunique.stderr.log",
+        shadow: 
+            "shallow"
+        threads: 1
+        conda:
+            "../../envs/stag-mwc.yaml",
+        container:
+            config["containers"]["stag"]
+        shell:
+            """
             workflow/scripts/plot_bbcountunique.py \
-              {output.txt} \
+              {input.txt} \
               {output.pdf} \
               >> {log.stdout} \
               2>> {log.stderr}
diff --git a/workflow/rules/naive/sketch_compare.smk b/workflow/rules/naive/sketch_compare.smk
index 3b6c831..987d9c5 100644
--- a/workflow/rules/naive/sketch_compare.smk
+++ b/workflow/rules/naive/sketch_compare.smk
@@ -1,6 +1,5 @@
 # vim: syntax=python expandtab
 # Compare all samples against all samples using MinHash sketches
-# TODO: Remove superfluous str conversions when Snakemake is pathlib compatible.
 
 localrules:
     compare_sketches,
@@ -10,7 +9,7 @@ localrules:
 if config["naive"]["sketch_compare"]:
     # Add final output files from this module to 'all_outputs' from the
     # main Snakefile scope.
-    sample_similarity_plot = str(OUTDIR/"sketch_compare/sample_similarity.pdf")
+    sample_similarity_plot = OUTDIR/"sketch_compare/sample_similarity.pdf"
     all_outputs.append(sample_similarity_plot)
 
     citations.add(publications["BBMap"])
@@ -24,13 +23,13 @@ rule sketch:
     output:
         sketch=OUTDIR/"sketch_compare/{sample}.sketch.gz",
     log:
-        str(LOGDIR/"sketch_compare/{sample}.sketch.log")
+        LOGDIR/"sketch_compare/{sample}.sketch.log",
     shadow: 
         "shallow"
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["bbmap"]
     threads: 4
     shell:
         """
@@ -45,18 +44,17 @@ rule sketch:
 rule compare_sketches:
     """Compare all samples using BBMap's comparesketch.sh"""
     input:
-        samples=expand(str(OUTDIR/"sketch_compare/{sample}.sketch.gz"), 
-                        sample=SAMPLES)
+        samples=expand(OUTDIR/"sketch_compare/{sample}.sketch.gz", sample=SAMPLES),
     output:
         alltoall=OUTDIR/"sketch_compare/alltoall.txt",
     log:
-        str(LOGDIR/"sketch_compare/comparesketch.log")
+        LOGDIR/"sketch_compare/comparesketch.log",
     shadow: 
         "shallow"
     conda: 
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["bbmap"]
     shell:
         """
         comparesketch.sh \
@@ -76,14 +74,14 @@ rule plot_sample_similarity:
         heatmap=OUTDIR/"sketch_compare/sample_similarity.pdf",
         clustered=report(OUTDIR/"sketch_compare/sample_similarity.clustered.pdf", 
                          category="Sketch comparison", 
-                         caption="../../report/sketch_compare.rst")
+                         caption="../../report/sketch_compare.rst"),
     log:
-        stdout=str(LOGDIR/"sketch_compare/sample_similarity_plot.stdout.log"),
-        stderr=str(LOGDIR/"sketch_compare/sample_similarity_plot.stderr.log"),
+        stdout=LOGDIR/"sketch_compare/sample_similarity_plot.stdout.log",
+        stderr=LOGDIR/"sketch_compare/sample_similarity_plot.stderr.log",
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/plot_sketch_comparison_heatmap.py \
diff --git a/workflow/rules/preproc/host_removal.smk b/workflow/rules/preproc/host_removal.smk
index 20c9ef2..c43f8bc 100644
--- a/workflow/rules/preproc/host_removal.smk
+++ b/workflow/rules/preproc/host_removal.smk
@@ -56,7 +56,7 @@ if config["host_removal"]["kraken2"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["kraken2"]
         threads: 8
         params:
             db=rh_kraken2["db_path"],
@@ -79,8 +79,7 @@ if config["host_removal"]["kraken2"]:
                 {params.extra} \
                 {input.read1} {input.read2} \
                 2> {log.stderr}
-            pigz \
-                --processes {threads} \
+            gzip \
                 --verbose \
                 --force \
                 {params.fq_to_compress} \
@@ -109,7 +108,7 @@ if config["host_removal"]["kraken2"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["stag"]
         threads: 1
         shell:
             """
@@ -155,7 +154,7 @@ if config["host_removal"]["bowtie2"]:
         conda:
             "../../envs/metaphlan.yaml"
         container:
-            "docker://quay.io/biocontainers/bowtie2:2.5.1--py38he00c5e5_2"
+            config["containers"]["bowtie2"]
         params:
             db_path=rh_bowtie2["db_path"],
             extra=rh_bowtie2["extra"],
@@ -183,7 +182,7 @@ if config["host_removal"]["bowtie2"]:
         conda:
             "../../envs/metaphlan.yaml"
         container:
-            "docker://quay.io/biocontainers/samtools:1.17--hd87286a_1"
+            config["containers"]["samtools"]
         shell:
             """
             samtools view \
@@ -207,7 +206,7 @@ if config["host_removal"]["bowtie2"]:
         conda:
             "../../envs/metaphlan.yaml"
         container:
-            "docker://quay.io/biocontainers/samtools:1.17--hd87286a_1"
+            config["containers"]["samtools"]
         shell:
             """
             samtools view \
@@ -233,7 +232,7 @@ if config["host_removal"]["bowtie2"]:
         conda:
             "../../envs/metaphlan.yaml"
         container:
-            "docker://quay.io/biocontainers/samtools:1.17--hd87286a_1"
+            config["containers"]["samtools"]
         shell: 
             """
             samtools sort \
@@ -259,7 +258,7 @@ if config["host_removal"]["bowtie2"]:
         conda:
             "../../envs/metaphlan.yaml"
         container:
-            "docker://quay.io/biocontainers/samtools:1.17--hd87286a_1"
+            config["containers"]["samtools"]
         shell: 
             """
             samtools fastq \
diff --git a/workflow/rules/preproc/preprocessing_summary.smk b/workflow/rules/preproc/preprocessing_summary.smk
index efa4fcb..c3c1349 100644
--- a/workflow/rules/preproc/preprocessing_summary.smk
+++ b/workflow/rules/preproc/preprocessing_summary.smk
@@ -29,7 +29,7 @@ rule preprocessing_summary:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     threads: 1
     params:
         fastp_arg=lambda w: f"--fastp {LOGDIR}/fastp/*.fastp.json" if config["qc_reads"] else "",
diff --git a/workflow/rules/preproc/read_quality.smk b/workflow/rules/preproc/read_quality.smk
index b93cd28..0584094 100644
--- a/workflow/rules/preproc/read_quality.smk
+++ b/workflow/rules/preproc/read_quality.smk
@@ -33,7 +33,7 @@ if config["qc_reads"]:
         conda:
             "../../envs/stag-mwc.yaml"
         container:
-            "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+            config["containers"]["fastp"]
         threads: 4
         params:
             extra=fastp_config["extra"],
diff --git a/workflow/rules/taxonomic_profiling/kaiju.smk b/workflow/rules/taxonomic_profiling/kaiju.smk
index 37bb6ba..ddb5288 100644
--- a/workflow/rules/taxonomic_profiling/kaiju.smk
+++ b/workflow/rules/taxonomic_profiling/kaiju.smk
@@ -18,7 +18,6 @@ if config["taxonomic_profile"]["kaiju"]:
                 Path(kaiju_config["names"]).exists()]):
         err_message = "No Kaiju database files at: '{}', '{}', '{}'!\n".format(kaiju_config["db"], kaiju_config["nodes"], kaiju_config["names"])
         err_message += "Specify relevant paths in the kaiju section of config.yaml.\n"
-        err_message += "Run 'snakemake download_kaiju_database' to download a copy into '{dbdir}'\n".format(dbdir=DBDIR/"kaiju") 
         err_message += "If you do not want to run Kaiju for taxonomic profiling, set 'kaiju: False' in config.yaml"
         raise WorkflowError(err_message)
 
@@ -56,7 +55,7 @@ rule kaiju:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["kaiju"]
     params:
         db=kaiju_config["db"],
         nodes=kaiju_config["nodes"],
@@ -86,7 +85,7 @@ rule kaiju2krona:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["kaiju"]
     shell:
         """
         kaiju2krona \
@@ -109,7 +108,7 @@ rule create_kaiju_krona_plot:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["krona"]
     shell:
         """
         ktImportText \
@@ -132,7 +131,7 @@ rule kaiju_report:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["kaiju"]
     shell:
         """
         kaiju2table \
@@ -163,7 +162,7 @@ rule join_kaiju_reports:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/join_tables.py \
@@ -187,7 +186,7 @@ rule kaiju_area_plot:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/area_plot.py \
diff --git a/workflow/rules/taxonomic_profiling/kraken2.smk b/workflow/rules/taxonomic_profiling/kraken2.smk
index 260e91f..d657769 100644
--- a/workflow/rules/taxonomic_profiling/kraken2.smk
+++ b/workflow/rules/taxonomic_profiling/kraken2.smk
@@ -1,7 +1,6 @@
 # vim: syntax=python expandtab
 # Taxonomic classification of metagenomic reads using Kraken2 with abundance
 # estimation using Bracken
-# TODO: Remove superfluous str conversions when Snakemake is pathlib compatible.
 from pathlib import Path
 
 from snakemake.exceptions import WorkflowError
@@ -27,19 +26,18 @@ if config["taxonomic_profile"]["kraken2"]:
     if not (kraken2_config["db"] and Path(kraken2_config["db"]).exists()):
         err_message = "No Kraken2 database folder at: '{}'!\n".format(kraken2_config["db"])
         err_message += "Specify the path in the kraken2 section of config.yaml.\n"
-        err_message += "Run 'snakemake download_minikraken2' to download a copy into '{dbdir}'\n".format(dbdir=DBDIR/"kraken2") 
         err_message += "If you do not want to run kraken2 for taxonomic profiling, set 'kraken2: False' in config.yaml"
         raise WorkflowError(err_message)
 
     # Add Kraken2 output files to 'all_outputs' from the main Snakefile scope.
     # SAMPLES is also from the main Snakefile scope.
-    krakens = expand(str(OUTDIR/"kraken2/{sample}.kraken"), sample=SAMPLES)
-    kreports = expand(str(OUTDIR/"kraken2/{sample}.kreport"), sample=SAMPLES)
-    kreports_mpa_style = expand(str(OUTDIR/"kraken2/{sample}.mpa_style.txt"), sample=SAMPLES)
-    joined_kreport_mpa_style = str(OUTDIR/"kraken2/all_samples.kraken2.mpa_style.txt")
-    combined_kreport = str(OUTDIR/"kraken2/all_samples.kraken2.txt")
-    kraken_krona = str(OUTDIR/"kraken2/all_samples.kraken2.krona.html")
-    kraken_area_plot = str(OUTDIR/"kraken2/area_plot.kraken2.pdf")
+    krakens = expand(OUTDIR/"kraken2/{sample}.kraken", sample=SAMPLES)
+    kreports = expand(OUTDIR/"kraken2/{sample}.kreport", sample=SAMPLES)
+    kreports_mpa_style = expand(OUTDIR/"kraken2/{sample}.mpa_style.txt", sample=SAMPLES)
+    joined_kreport_mpa_style = OUTDIR/"kraken2/all_samples.kraken2.mpa_style.txt"
+    combined_kreport = OUTDIR/"kraken2/all_samples.kraken2.txt"
+    kraken_krona = OUTDIR/"kraken2/all_samples.kraken2.krona.html"
+    kraken_area_plot = OUTDIR/"kraken2/area_plot.kraken2.pdf"
 
     if kraken2_config["keep_kraken"]:
         all_outputs.extend(krakens)
@@ -64,14 +62,14 @@ rule kraken2:
         kraken=OUTDIR/"kraken2/{sample}.kraken" if kraken2_config["keep_kraken"] else temp(OUTDIR/"kraken2/{sample}.kraken"),
         kreport=OUTDIR/"kraken2/{sample}.kreport" if kraken2_config["keep_kreport"] else temp(OUTDIR/"kraken2/{sample}.kreport"),
     log:
-        str(LOGDIR/"kraken2/{sample}.kraken2.log")
+        LOGDIR/"kraken2/{sample}.kraken2.log"
     shadow: 
         "shallow"
     threads: 8
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["kraken2"]
     params:
         db=kraken2_config["db"],
         confidence=kraken2_config["confidence"],
@@ -96,16 +94,16 @@ rule kraken2:
 
 rule kraken_mpa_style:
     input:
-        kreport=OUTDIR/"kraken2/{sample}.kreport"
+        kreport=OUTDIR/"kraken2/{sample}.kreport",
     output:
         txt=OUTDIR/"kraken2/{sample}.mpa_style.txt",
     log:
-        str(LOGDIR/"kraken2/{sample}.mpa_style.log")
+        LOGDIR/"kraken2/{sample}.mpa_style.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/KrakenTools/kreport2mpa.py \
@@ -113,24 +111,25 @@ rule kraken_mpa_style:
             --output {output.txt} \
             --display-header \
             2>&1 > {log}
+
         sed --in-place 's|{input.kreport}|taxon_name\treads|g' {output.txt}
         """
 
 
 rule join_kraken2_mpa:
     input:
-        txt=expand(str(OUTDIR/"kraken2/{sample}.mpa_style.txt"), sample=SAMPLES),
+        txt=expand(OUTDIR/"kraken2/{sample}.mpa_style.txt", sample=SAMPLES),
     output:
         table=report(OUTDIR/"kraken2/all_samples.kraken2.mpa_style.txt",
                category="Taxonomic profiling",
                caption="../../report/kraken2_table_mpa.rst"),
     log:
-        str(LOGDIR/"kraken2/join_kraken2_mpa_tables.log")
+        LOGDIR/"kraken2/join_kraken2_mpa_tables.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     params:
         value_column="reads",
         feature_column="taxon_name",
@@ -147,17 +146,17 @@ rule join_kraken2_mpa:
 
 rule kraken2_area_plot:
     input:
-        OUTDIR/"kraken2/all_samples.kraken2.mpa_style.txt"
+        OUTDIR/"kraken2/all_samples.kraken2.mpa_style.txt",
     output:
         report(OUTDIR/"kraken2/area_plot.kraken2.pdf",
             category="Taxonomic profiling",
             caption="../../report/area_plot.rst")
     log:
-        str(LOGDIR/"kraken2/area_plot.kraken2.log")
+        LOGDIR/"kraken2/area_plot.kraken2.log",
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/area_plot.py \
@@ -170,19 +169,19 @@ rule kraken2_area_plot:
 
 rule combine_kreports:
     input:
-        kreports=expand(str(OUTDIR/"kraken2/{sample}.kreport"), sample=SAMPLES),
+        kreports=expand(OUTDIR/"kraken2/{sample}.kreport", sample=SAMPLES),
     output:
         report(OUTDIR/"kraken2/all_samples.kraken2.txt",
                category="Taxonomic profiling",
                caption="../../report/kraken2_table.rst"),
     log:
-        str(LOGDIR/"kraken2/combined_kreport.log")
+        LOGDIR/"kraken2/combined_kreport.log"
     shadow:
         "shallow"
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/KrakenTools/combine_kreports.py \
@@ -199,14 +198,14 @@ rule kreport2krona:
     output:
         OUTDIR/"kraken2/{sample}.krona"
     log:
-        str(LOGDIR/"kraken2/{sample}.kreport2krona.log")
+        LOGDIR/"kraken2/{sample}.kreport2krona.log",
     shadow: 
         "shallow"
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/KrakenTools/kreport2krona.py \
@@ -218,7 +217,7 @@ rule kreport2krona:
 
 rule create_kraken2_krona_plot:
     input:
-        expand(str(OUTDIR/"kraken2/{sample}.krona"), sample=SAMPLES),
+        expand(OUTDIR/"kraken2/{sample}.krona", sample=SAMPLES),
     output:
         krona_html=report(OUTDIR/"kraken2/all_samples.kraken2.krona.html",
                           category="Taxonomic profiling",
@@ -228,7 +227,7 @@ rule create_kraken2_krona_plot:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["krona"]
     shell:
         """
 		ktImportText \
@@ -241,13 +240,12 @@ if config["taxonomic_profile"]["kraken2"] and kraken2_config["bracken"]["kmer_di
     if not Path(kraken2_config["bracken"]["kmer_distrib"]).exists():
         err_message = "No Bracken kmer_distrib database file at: '{}'!\n".format(kraken2_config["bracken"]["kmer_distrib"])
         err_message += "Specify the path in the kraken2 section of config.yaml.\n"
-        err_message += "Run 'snakemake download_minikraken2' to download a copy of the required files into '{dbdir}'\n".format(dbdir=DBDIR/"kraken2") 
         err_message += "If you do not want to run Bracken for abundance profiling, set 'kmer_distrib: ""' in the bracken section of config.yaml"
         raise WorkflowError(err_message)
     if kraken2_config["filter_bracken"]["include"] or kraken2_config["filter_bracken"]["exclude"]:
-        filtered_brackens = expand(str(OUTDIR/"kraken2/{sample}.{level}.filtered.bracken"), sample=SAMPLES, level=kraken2_config["bracken"]["levels"].split())
-        all_table = expand(str(OUTDIR/"kraken2/all_samples.{level}.bracken.txt"), level=kraken2_config["bracken"]["levels"].split())
-        all_table_filtered = expand(str(OUTDIR/"kraken2/all_samples.{level}.filtered.bracken.txt"), level=kraken2_config["bracken"]["levels"].split())
+        filtered_brackens = expand(OUTDIR/"kraken2/{sample}.{level}.filtered.bracken", sample=SAMPLES, level=kraken2_config["bracken"]["levels"].split())
+        all_table = expand(OUTDIR/"kraken2/all_samples.{level}.bracken.txt", level=kraken2_config["bracken"]["levels"].split())
+        all_table_filtered = expand(OUTDIR/"kraken2/all_samples.{level}.filtered.bracken.txt", level=kraken2_config["bracken"]["levels"].split())
 
         all_outputs.extend(filtered_brackens)
         all_outputs.append(all_table)
@@ -255,11 +253,11 @@ if config["taxonomic_profile"]["kraken2"] and kraken2_config["bracken"]["kmer_di
 
     citations.add(publications["Bracken"])
 
-    brackens = expand(str(OUTDIR/"kraken2/{sample}.{level}.bracken"), sample=SAMPLES, level=kraken2_config["bracken"]["levels"].split())
-    brackens_mpa_style = expand(str(OUTDIR/"kraken2/{sample}.bracken.mpa_style.txt"), sample=SAMPLES)
-    bracken_area_plot = str(OUTDIR/"kraken2/area_plot.bracken.pdf")
-    bracken_krona = str(OUTDIR/"kraken2/all_samples.bracken.krona.html")
-    all_table_mpa = str(OUTDIR/"kraken2/all_samples.bracken.mpa_style.txt")
+    brackens = expand(OUTDIR/"kraken2/{sample}.{level}.bracken", sample=SAMPLES, level=kraken2_config["bracken"]["levels"].split())
+    brackens_mpa_style = expand(OUTDIR/"kraken2/{sample}.bracken.mpa_style.txt", sample=SAMPLES)
+    bracken_area_plot = OUTDIR/"kraken2/area_plot.bracken.pdf"
+    bracken_krona = OUTDIR/"kraken2/all_samples.bracken.krona.html"
+    all_table_mpa = OUTDIR/"kraken2/all_samples.bracken.mpa_style.txt"
 
     all_outputs.extend(brackens)
     all_outputs.extend(brackens_mpa_style)
@@ -272,19 +270,19 @@ rule bracken_kreport:
     """Run Bracken summarization for Species level to get total sample
     bracken.kreport (required for mpa-conversion later)."""
     input:
-        kreport=OUTDIR/"kraken2/{sample}.kreport"
+        kreport=OUTDIR/"kraken2/{sample}.kreport",
     output:
         bracken=OUTDIR/"kraken2/{sample}.bracken",
         bracken_kreport=OUTDIR/"kraken2/{sample}_bracken.kreport",
     log:
-        str(LOGDIR/"kraken2/{sample}.bracken.log")
+        LOGDIR/"kraken2/{sample}.bracken.log",
     threads: 2
     shadow:
         "shallow"
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["bracken"]
     params:
         kmer_distrib=kraken2_config["bracken"]["kmer_distrib"],
         thresh=kraken2_config["bracken"]["thresh"],
@@ -304,18 +302,18 @@ rule bracken_kreport:
 rule bracken_all_levels:
     """Run Bracken summarization for all levels."""
     input:
-        kreport=OUTDIR/"kraken2/{sample}.kreport"
+        kreport=OUTDIR/"kraken2/{sample}.kreport",
     output:
         bracken=OUTDIR/"kraken2/{sample}.{level,[DPOCFGS]}.bracken",
     log:
-        str(LOGDIR/"kraken2/{sample}.{level}.bracken.log")
+        LOGDIR/"kraken2/{sample}.{level}.bracken.log",
     shadow:         # shadow required because est_abundance.py always creates the
         "shallow"   # sample-level output file with fixed filename: {sample}_bracken.kreport 
     threads: 2
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["bracken"]
     params:
         kmer_distrib=kraken2_config["bracken"]["kmer_distrib"],
         thresh=kraken2_config["bracken"]["thresh"],
@@ -333,16 +331,16 @@ rule bracken_all_levels:
 
 rule bracken_mpa_style:
     input:
-        kreport=OUTDIR/"kraken2/{sample}_bracken.kreport"
+        kreport=OUTDIR/"kraken2/{sample}_bracken.kreport",
     output:
         txt=OUTDIR/"kraken2/{sample}.bracken.mpa_style.txt",
     log:
-        str(LOGDIR/"kraken2/{sample}.bracken.mpa_style.log")
+        LOGDIR/"kraken2/{sample}.bracken.mpa_style.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/KrakenTools/kreport2mpa.py \
@@ -350,24 +348,25 @@ rule bracken_mpa_style:
             --output {output.txt} \
             --display-header \
             2>&1 > {log}
+
         sed --in-place 's|{input.kreport}|taxon_name\treads|g' {output.txt}
         """
 
 
 rule join_bracken_mpa:
     input:
-        txt=expand(str(OUTDIR/"kraken2/{sample}.bracken.mpa_style.txt"), sample=SAMPLES),
+        txt=expand(OUTDIR/"kraken2/{sample}.bracken.mpa_style.txt", sample=SAMPLES),
     output:
         table=report(OUTDIR/"kraken2/all_samples.bracken.mpa_style.txt",
                category="Taxonomic profiling",
                caption="../../report/bracken_table_mpa.rst"),
     log:
-        str(LOGDIR/"kraken2/join_bracken_mpa_tables.log")
+        LOGDIR/"kraken2/join_bracken_mpa_tables.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     params:
         value_column="reads",
         feature_column="taxon_name",
@@ -390,11 +389,11 @@ rule bracken_area_plot:
             category="Taxonomic profiling",
             caption="../../report/area_plot.rst")
     log:
-        str(LOGDIR/"kraken2/area_plot.bracken.log")
+        LOGDIR/"kraken2/area_plot.bracken.log",
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/area_plot.py \
@@ -407,18 +406,18 @@ rule bracken_area_plot:
 
 rule join_bracken:
     input:
-        bracken=expand(str(OUTDIR/"kraken2/{sample}.{{level}}.bracken"), sample=SAMPLES),
+        bracken=expand(OUTDIR/"kraken2/{sample}.{{level}}.bracken", sample=SAMPLES),
     output:
         table=report(OUTDIR/"kraken2/all_samples.{level,[DPOCFGS]}.bracken.txt",
                category="Taxonomic profiling",
                caption="../../report/bracken_table.rst"),
     log:
-        str(LOGDIR/"kraken2/join_bracken_tables.{level}.log")
+        LOGDIR/"kraken2/join_bracken_tables.{level}.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     params:
         value_column="fraction_total_reads",
         feature_column="name",
@@ -439,14 +438,14 @@ rule bracken2krona:
     output:
         bracken_krona=OUTDIR/"kraken2/{sample}.bracken.krona",
     log:
-        str(LOGDIR/"kraken2/{sample}.bracken2krona.log")
+        LOGDIR/"kraken2/{sample}.bracken2krona.log",
     threads: 1
     shadow:
         "shallow"
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/KrakenTools/kreport2krona.py \
@@ -458,7 +457,7 @@ rule bracken2krona:
 
 rule create_bracken_krona_plot:
     input:
-        expand(str(OUTDIR/"kraken2/{sample}.bracken.krona"), sample=SAMPLES),
+        expand(OUTDIR/"kraken2/{sample}.bracken.krona", sample=SAMPLES),
     output:
         krona_html=report(OUTDIR/"kraken2/all_samples.bracken.krona.html",
                           category="Taxonomic profiling",
@@ -468,7 +467,7 @@ rule create_bracken_krona_plot:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["krona"]
     shell:
         """
 		ktImportText \
@@ -483,12 +482,12 @@ rule filter_bracken:
     output:
         filtered=OUTDIR/"kraken2/{sample}.{level,[DPOCFGS]}.filtered.bracken",  
     log:
-        str(LOGDIR/"kraken2/{sample}.{level}.filter_bracken.log")
+        LOGDIR/"kraken2/{sample}.{level}.filter_bracken.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     params:
         filter_bracken="workflow/scripts/KrakenTools/filter_bracken.out.py",
         include=kraken2_config["filter_bracken"]["include"],
@@ -506,18 +505,18 @@ rule filter_bracken:
 
 rule join_bracken_filtered:
     input:
-        bracken=expand(str(OUTDIR/"kraken2/{sample}.{{level}}.filtered.bracken"), sample=SAMPLES),
+        bracken=expand(OUTDIR/"kraken2/{sample}.{{level}}.filtered.bracken", sample=SAMPLES),
     output:
         table=report(OUTDIR/"kraken2/all_samples.{level,[DPCOFGS]}.filtered.bracken.txt",
                category="Taxonomic profiling",
                caption="../../report/bracken_table_filtered.rst"),
     log:
-        str(LOGDIR/"kraken2/join_bracken_tables.{level}.log")
+        LOGDIR/"kraken2/join_bracken_tables.{level}.log",
     threads: 1
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     params:
         value_column="fraction_total_reads",
         feature_column="name",
@@ -530,3 +529,4 @@ rule join_bracken_filtered:
             {input.bracken} \
             2>&1 > {log}
         """
+
diff --git a/workflow/rules/taxonomic_profiling/krakenuniq.smk b/workflow/rules/taxonomic_profiling/krakenuniq.smk
index bc5a0a1..d64dc5a 100644
--- a/workflow/rules/taxonomic_profiling/krakenuniq.smk
+++ b/workflow/rules/taxonomic_profiling/krakenuniq.smk
@@ -54,7 +54,7 @@ rule krakenuniq_merge_reads:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["bbmap"]
     shell:
         """
         fuse.sh \
@@ -80,7 +80,7 @@ rule krakenuniq:
     conda:
         "../../envs/krakenuniq.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:krakenuniq"+singularity_branch_tag
+        config["containers"]["krakenuniq"]
     params:
         db=krakenuniq_config["db"],
         preload_size=krakenuniq_config["preload_size"],
@@ -114,7 +114,7 @@ rule krakenuniq_combine_reports:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/join_tables.py \
@@ -139,7 +139,7 @@ rule krakenuniq_mpa_style:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/KrakenTools/kreport2mpa.py \
@@ -165,7 +165,7 @@ rule krakenuniq_join_mpa:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     params:
         value_column="reads",
         feature_column="taxon_name",
@@ -195,7 +195,7 @@ rule krakenuniq_kreport2krona:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         awk -v OFS='\\t' '{{
@@ -220,7 +220,7 @@ rule krakenuniq_krona_plot:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["krona"]
     shell:
         """
 		ktImportText \
diff --git a/workflow/rules/taxonomic_profiling/metaphlan.smk b/workflow/rules/taxonomic_profiling/metaphlan.smk
index 83346d6..94b858e 100644
--- a/workflow/rules/taxonomic_profiling/metaphlan.smk
+++ b/workflow/rules/taxonomic_profiling/metaphlan.smk
@@ -56,7 +56,7 @@ rule metaphlan:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "docker://quay.io/biocontainers/metaphlan:4.0.6--pyhca03a8a_0"
+        config["containers"]["metaphlan"]
     threads: 8
     params:
         bt2_db_dir=mpa_config["bt2_db_dir"],
@@ -118,7 +118,7 @@ rule combine_metaphlan_tables:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "docker://quay.io/biocontainers/metaphlan:4.0.6--pyhca03a8a_0"
+        config["containers"]["metaphlan"]
     threads: 1
     shell:
         """
@@ -139,7 +139,7 @@ rule metaphlan_area_plot:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     shell:
         """
         workflow/scripts/area_plot.py \
@@ -165,7 +165,7 @@ rule plot_metaphlan_heatmap:
     conda:
         "../../envs/stag-mwc.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["stag"]
     threads: 1
     params:
         outfile_prefix=lambda w: f"{OUTDIR}/metaphlan/all_samples",
@@ -206,7 +206,7 @@ rule create_metaphlan_krona_plots:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag
+        config["containers"]["krona"]
     threads: 1
     shell:
         """
diff --git a/workflow/rules/taxonomic_profiling/strainphlan.smk b/workflow/rules/taxonomic_profiling/strainphlan.smk
index 13bc24a..af64cff 100644
--- a/workflow/rules/taxonomic_profiling/strainphlan.smk
+++ b/workflow/rules/taxonomic_profiling/strainphlan.smk
@@ -45,7 +45,7 @@ rule consensus_markers:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["metaphlan"]
     threads: 8
     params:
         output_dir=f"{OUTDIR}/strainphlan/consensus_markers/{{sample}}"
@@ -73,7 +73,7 @@ rule print_clades:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["metaphlan"]
     threads: 8
     params:
         out_dir=f"{OUTDIR}/strainphlan",
@@ -107,7 +107,7 @@ rule extract_markers:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["metaphlan"]
     threads: 8
     params:
         clade=spa_config["clade_of_interest"],
@@ -139,7 +139,7 @@ rule strainphlan:
     conda:
         "../../envs/metaphlan.yaml"
     container:
-        "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag
+        config["containers"]["metaphlan"]
     threads: 8
     params:
         clade=spa_config["clade_of_interest"],
@@ -149,7 +149,7 @@ rule strainphlan:
         extra=spa_config["extra"],  # This is extremely useful if you want to include a reference genome
     shell:
         """
-        echo "please compare your clade_of_interest to list of available clades in available_clades.txt" > {log.stderr}
+        echo "Please compare your clade_of_interest to list of available clades in available_clades.txt" > {log.stderr}
 
         strainphlan \
              -s {input.consensus_markers} \
diff --git a/workflow/scripts/amrplusplus/LICENSE b/workflow/scripts/amrplusplus/LICENSE
deleted file mode 100644
index f0f3790..0000000
--- a/workflow/scripts/amrplusplus/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2017 Chris Dean
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
diff --git a/workflow/scripts/amrplusplus/amr_long_to_wide.py b/workflow/scripts/amrplusplus/amr_long_to_wide.py
deleted file mode 100755
index 0d4d1ca..0000000
--- a/workflow/scripts/amrplusplus/amr_long_to_wide.py
+++ /dev/null
@@ -1,67 +0,0 @@
-#!/usr/bin/env python3
-
-__author__ = "Steven Lakin"
-__copyright__ = ""
-__credits__ = ["Steven Lakin"]
-__version__ = ""
-__maintainer__ = "lakinsm"
-__email__ = "lakinsm@colostate.edu"
-__status__ = "Cows go moo."
-
-import argparse
-import sys
-
-amr_level_names = {0: 'Class', 1: 'Mechanism', 2: 'Group'}
-
-def parse_cmdline_params(cmdline_params):
-    info = ""
-    parser = argparse.ArgumentParser(description=info)
-    parser.add_argument('-i', '--input_files', nargs='+', required=True,
-                        help='Use globstar to pass a list of files, (Ex: *.tsv)')
-    parser.add_argument('-o', '--output_file', required=True,
-                        help='Output file name for writing the AMR_analytic_matrix.csv file')
-    return parser.parse_args(cmdline_params)
-
-def amr_load_data(file_name_list):
-    samples = {}
-    labels = set()
-    for file in file_name_list:
-        with open(file, 'r') as f:
-            data = f.read().split('\n')[1:]
-            for entry in data:
-                if not entry:
-                    continue
-                entry = entry.split('\t')
-                sample = entry[0].split('.')[0]
-                count = float(entry[2])
-                gene_name = entry[1]
-                try:
-                    samples[sample][gene_name] = count
-                except KeyError:
-                    try:
-                        samples[sample].setdefault(gene_name, count)
-                    except KeyError:
-                        samples.setdefault(sample, {gene_name: count})
-                labels.add(gene_name)
-    return samples, labels
-
-def output_amr_analytic_data(outfile, S, L):
-    with open(outfile, 'w') as amr:
-        local_sample_names = []
-        for sample, dat in S.items():
-            local_sample_names.append(sample)
-        amr.write(','.join(local_sample_names) + '\n')
-        for label in L:
-            local_counts = []
-            amr.write(label + ',')
-            for local_sample in local_sample_names:
-                if label in S[local_sample]:
-                    local_counts.append(str(S[local_sample][label]))
-                else:
-                    local_counts.append(str(0))
-            amr.write(','.join(local_counts) + '\n')
-
-if __name__ == '__main__':
-    opts = parse_cmdline_params(sys.argv[1:])
-    S, L = amr_load_data(opts.input_files)
-    output_amr_analytic_data(opts.output_file, S, L)
diff --git a/workflow/scripts/amrplusplus/rarefaction b/workflow/scripts/amrplusplus/rarefaction
deleted file mode 100755
index 4ad5eca..0000000
Binary files a/workflow/scripts/amrplusplus/rarefaction and /dev/null differ
diff --git a/workflow/scripts/amrplusplus/resistome b/workflow/scripts/amrplusplus/resistome
deleted file mode 100755
index d7bc642..0000000
Binary files a/workflow/scripts/amrplusplus/resistome and /dev/null differ