diff --git a/acanthophis/template/workflow/config.schema.yml b/acanthophis/template/workflow/config.schema.yml
index 2121aec..a6a3f17 100644
--- a/acanthophis/template/workflow/config.schema.yml
+++ b/acanthophis/template/workflow/config.schema.yml
@@ -32,10 +32,10 @@ properties:
         additionalProperties:
           type: object
           properties:
-            nodes:
-              type: string
-            fmi:
+            dir:
               type: string
+            bracken:
+              type: integer
             required:
               - dir
               - bracken
diff --git a/acanthophis/template/workflow/rules/align.rules b/acanthophis/template/workflow/rules/align.rules
index 4eed406..a0abd95 100644
--- a/acanthophis/template/workflow/rules/align.rules
+++ b/acanthophis/template/workflow/rules/align.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -22,6 +22,7 @@ rule ngmap_idx:
         L("{path}-index.log"),
     resources: **rule_resources(config, "ngmap_idx", runtime=40, mem_gb=2, cores=1)
     conda: "envs/align.yml"
+    container: "docker://ghcr.io/kdm9/align:latest"
     shell:
         "( ngm"
         "   -r {input.ref}"
@@ -39,6 +40,7 @@ rule ngmap:
     resources: **rule_resources(config, "ngmap", runtime=240, mem_gb=16, cores=8)
     params:
         sensitivity=config["tool_settings"]["ngm"]["sensitivity"],
+    container: "docker://ghcr.io/kdm9/align:latest"
     conda: "envs/align.yml"
     shell:
         "( ngm"
@@ -66,6 +68,7 @@ rule bwaidx:
         R("{path}.pac"),
         R("{path}.sa"),
     conda: "envs/align.yml"
+    container: "docker://ghcr.io/kdm9/align:latest"
     log: L("{path}_index.log"),
     resources: **rule_resources(config, "bwaidx", runtime=20, mem_gb=8)
     shell:
@@ -85,6 +88,7 @@ rule bwamem:
         bam=temp(T("alignments/byrun.raw/bwa/{ref}/{run}~{lib}~{sample}.bam")),
     log: L("alignments/byrun.raw/bwa/{ref}/{run}~{lib}~{sample}.bam.log")
     resources: **rule_resources(config, "bwamem", runtime=240, mem_gb=10, cores=8)
+    container: "docker://ghcr.io/kdm9/align:latest"
     conda: "envs/align.yml"
     shell:
         "( bwa mem"
@@ -112,6 +116,7 @@ rule bam_merge_markdups_sort:
     resources: **rule_resources(config, "bam_merge_markdups_sort", runtime=240, mem_gb=16, disk_gb=50, cores=8)
     log: L("alignments/samples/{aligner}~{ref}~{sample}.bam.log")
     conda: "envs/align.yml"
+    container: "docker://ghcr.io/kdm9/align:latest"
     priority: 2
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
@@ -169,6 +174,7 @@ rule mergebam_set:
     log:
         L("alignments/sets/{aligner}~{ref}~{sampleset}.bam.log"),
     resources: **rule_resources(config, "mergebam_set", runtime=2880, mem_gb=16, disk_gb=1000, cores=64)
+    container: "docker://ghcr.io/kdm9/align:latest"
     conda: "envs/align.yml"
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
@@ -195,6 +201,7 @@ rule bamstat_sample:
         L("alignments/bamstats/sample/{aligner}~{ref}~{sample}.samtools.stats.log")
     resources: **rule_resources(config, "bamstat_sample", runtime=120, mem_gb=4, cores=1)
     conda: "envs/align.yml"
+    container: "docker://ghcr.io/kdm9/align:latest"
     shell:
         "(samtools stats -i 5000 -x {input} >{output}) >{log} 2>&1"
 
@@ -208,6 +215,7 @@ rule multiqc_samstats:
         log=L("stats/multiqc/bamstats_{aligner}~{ref}~{sampleset}_multiqc.log"),
     resources: **rule_resources(config, "multiqc_samstats", runtime=30, mem_gb=2, cores=1)
     conda: "envs/qcstats.yml"
+    container: "docker://multiqc/multiqc:v1.20"
     shell:
         "multiqc"
         "   --no-megaqc-upload"
@@ -251,6 +259,7 @@ rule multiqc_qualimap:
         log=L("stats/multiqc/qualimap_{aligner}~{ref}~{sampleset}_multiqc.log"),
     resources: **rule_resources(config, "multiqc_qualimap", runtime=30, mem_gb=2, cores=1)
     conda: "envs/qcstats.yml"
+    container: "docker://multiqc/multiqc:v1.20"
     shell:
         "multiqc"
         "   --no-megaqc-upload"
@@ -276,6 +285,7 @@ rule extract_unmapped:
         L("alignments/unmapped_reads/{aligner}~{ref}~{sample}.fastq.gz.log"),
     resources: **rule_resources(config, "extract_unmapped", runtime=120, mem_gb=1, cores=8)
     conda: "envs/align.yml"
+    container: "docker://ghcr.io/kdm9/align:latest"
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     shell:
diff --git a/acanthophis/template/workflow/rules/base.rules b/acanthophis/template/workflow/rules/base.rules
index f3c4a62..5a4a63f 100644
--- a/acanthophis/template/workflow/rules/base.rules
+++ b/acanthophis/template/workflow/rules/base.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -101,12 +101,11 @@ def parse_metadata(s2rl_file):
         if s2rl_file.endswith(".tsv"):
             dialect = "excel-tab"
         for run in csv.DictReader(fh, dialect=dialect):
-            if not run["library"] or run["library"].lower().startswith("blank"):
-                # Skip blanks
-                continue
             if run.get("include", "Y").upper() != "Y" or run.get("exclude", "N").upper() == "Y":
                 # Remove non-sequenced ones
                 continue
+            if run.get("exclude_why", ""):
+                continue
             meta.append({k.lower(): v for k, v in run.items()})
     return meta
 
@@ -119,6 +118,7 @@ def make_runlib2samp(rl2s_meta):
         samp = run["sample"]
         rl2s[rl] = samp
         s2rl[samp].append(rl)
+    print(f"Parsed {len(rl2s)} run-libs from {len(s2rl)} samples")
     return dict(rl2s), dict(s2rl)
 
 
diff --git a/acanthophis/template/workflow/rules/deepvariant.rules b/acanthophis/template/workflow/rules/deepvariant.rules
index b50e3d0..a3e353c 100644
--- a/acanthophis/template/workflow/rules/deepvariant.rules
+++ b/acanthophis/template/workflow/rules/deepvariant.rules
@@ -1,3 +1,13 @@
+# These rules are part of Acanthophis. See https://github.com/kdm9/Acanthophis.
+# This file *could* be modified, but then be careful when you update them. And
+# please, if you find a bug, raise an issue on github so the fix gets shared
+# with everyone.
+#
+# Copyright 2020-2024 Kevin Murray/Gekkonid Consulting
+#
+# This Source Code Form is subject to the terms of the Mozilla Public License,
+# v. 2.0. If a copy of the MPL was not distributed with this file, You can
+# obtain one at http://mozilla.org/MPL/2.0/.
 
 rule deepvariant_gvcf:
     input:
@@ -17,7 +27,7 @@ rule deepvariant_gvcf:
         model=lambda wc: config["tool_settings"]["varcall"].get("deepvariant_model", "WGS"),
         extra="",
     shadow: "shallow"
-    resources: **rule_resources(config, "deepvariant_gvcf", runtime=600, mem_gb=96, cores=48, disk_mb=400_000)
+    resources: **rule_resources(config, "deepvariant_gvcf", runtime=600, mem_gb=96, cores=32, disk_mb=400_000)
     shell:
         "( /opt/deepvariant/bin/run_deepvariant"
         "   --model_type={params.model}"
@@ -29,29 +39,6 @@ rule deepvariant_gvcf:
         "   --intermediate_results_dir=$TMPDIR"
         "   --num_shards={threads}"
         ") &> {log}"
-        #"( mkdir -p {params.tmp_dir}"
-        #" && dv_make_examples.py"
-        #"   --cores {threads}"
-        #"   --ref {input.ref}"
-        #"   --reads {input.bam}"
-        #"   --sample {wildcards.sample}"
-        #"   --examples {params.tmp_dir}"
-        #"   --logdir {params.tmp_dir}" 
-        #"   --gvcf {params.tmp_dir}"
-        #"   {params.extra}"
-        #" && dv_call_variants.py"
-        #"   --cores {threads}"
-        #"   --outfile {params.tmp_dir}/{wc.sample}.calls"
-        #"   --sample {wildcards.sample} "
-        #"   --examples {params.tmp_dir}"
-        #"   --model {params.model}"
-        #"&& dv_postprocess_variants.py "
-        #"   --ref {input.ref} "
-        #"   --gvcf_infile {params.tmp_dir}/{wc.sample}.gvcf.tfrecord@{threads}.gz"
-        #"   --gvcf_outfile {output.gvcf} "
-        #"   --infile {params.tmp_dir}/{wc.sample}.calls"
-        #"   --outfile {output.vcf}"
-        #") &> {log}"
 
 
 localrules: glnexus_fofn
@@ -79,10 +66,10 @@ rule glnexus_call:
         T("deepvariant/{aligner}~{ref}~{sampleset}.vcf.gz.log"),
     conda:
         "envs/glnexus.yml",
-    #container:
-    #    "docker://ghcr.io/dnanexus-rnd/glnexus:v1.4.1"
+    container:
+        "docker://ghcr.io/kdm9/glnexus-bcftools:latest"
     shadow: "shallow"
-    resources: **rule_resources(config, "glnexus_call", runtime=180, mem_gb=128, cores=128)
+    resources: **rule_resources(config, "glnexus_call", runtime=180, mem_gb=512, cores=128)
     shell:
         "( glnexus_cli"
         "   --config DeepVariant"
diff --git a/acanthophis/template/workflow/rules/denovo.rules b/acanthophis/template/workflow/rules/denovo.rules
index 2d6efb2..9ee3947 100644
--- a/acanthophis/template/workflow/rules/denovo.rules
+++ b/acanthophis/template/workflow/rules/denovo.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -65,6 +65,7 @@ rule mash_sketch_set:
     log: L("mash/{set}~k{ksize}~s{sketchsize}.sketch.msh.log")
     resources: **rule_resources(config, "mash_sketch_set", runtime=2880, mem_gb=16, cores=48)
     conda: "envs/mash.yml"
+    container: "docker://ghcr.io/kdm9/mash:latest"
     shell:
         " mash sketch"
         "   -k {wildcards.ksize}"
@@ -84,6 +85,7 @@ rule mash_dist_set:
         L("mash/{set}~k{ksize}~s{sketchsize}.dist.log")
     resources: **rule_resources(config, "mash_dist_set", runtime=2880, mem_gb=16, cores=48)
     conda: "envs/mash.yml"
+    container: "docker://ghcr.io/kdm9/mash:latest"
     shell:
         "mash dist"
         "   -p {threads}"
diff --git a/acanthophis/template/workflow/rules/metagenome.rules b/acanthophis/template/workflow/rules/metagenome.rules
index 9396c01..73ea965 100644
--- a/acanthophis/template/workflow/rules/metagenome.rules
+++ b/acanthophis/template/workflow/rules/metagenome.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -53,12 +53,13 @@ rule diamondx_reads2db:
         db=lambda wc: R(config["data_paths"]["diamond"][wc.db]),
         reads=diamondx_reads2db_input,
     output:
-        tsv=P("metagenome/diamondx/{type}/{sample}~{db}.tsv.xz"),
+        tsv=P("metagenome/diamondx/{type}/{sample}~{db}.tsv.zstd"),
     log:
         L("metagenome/diamondx/{type}/{sample}~{db}.tsv.log"),
     benchmark: 
         L("metagenome/diamondx/{type}/{sample}~{db}.tsv.bench.csv"),
     conda: "envs/diamond.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-diamond:latest"
     resources: **rule_resources(config, "diamondx_reads2db", runtime=7200, mem_gb=72, disk_gb=5, cores=24)
     shell:
         'T=/tmp/holopipe_$RANDOM; mkdir -p $T; trap "rm -rf $T" INT EXIT TERM;'
@@ -73,7 +74,7 @@ rule diamondx_reads2db:
         "   --index-chunks 4"
         "   --tmpdir $T"
         "   --ignore-warnings"
-        "   --out >(xz -T{threads} >{output.tsv})"
+        "   --out >(zstd -T{threads} >{output.tsv})"
         " &> {log}"
 
 rule humann:
@@ -196,6 +197,7 @@ rule plass_quant_diamond:
         L("metagenome/plass/{type}/{samplelike}~renamed.faa.quant.blast.tsv.log"),
     benchmark: L("metagenome/plass/{type}/{samplelike}~renamed.faa.quant.blast.tsv.bench.csv"),
     conda: "envs/diamond.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-diamond:latest"
     resources: **rule_resources(config, "plass_quant_diamond", runtime=1440, mem_gb=90, disk_gb=16, cores=32)
     shell:
         "diamond blastx"
@@ -220,6 +222,7 @@ rule plass_diamond:
         L("metagenome/plass/{path}.{db}.blasttab.log")
     benchmark: P("metagenome/plass/{path}.{db}.blasttab.bench.csv")
     conda: "envs/diamond.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-diamond:latest"
     resources: **rule_resources(config, "plass_diamond", runtime=1440, mem_gb=90, disk_gb=16, cores=32)
     shell:
         "diamond blastp"
@@ -298,7 +301,7 @@ rule all_megahit:
 
 rule all_diamondx:
     input:
-        [P(f"metagenome/diamondx/{type}/{sample}~{db}.tsv.xz")
+        [P(f"metagenome/diamondx/{type}/{sample}~{db}.tsv.zstd")
            for sampleset in config["samplesets"]
            for sample in config["SAMPLESETS"][sampleset]
            for type in config["samplesets"][sampleset].get("diamondx", {}).get("types", [])
diff --git a/acanthophis/template/workflow/rules/reads.rules b/acanthophis/template/workflow/rules/reads.rules
index a118c20..076126b 100644
--- a/acanthophis/template/workflow/rules/reads.rules
+++ b/acanthophis/template/workflow/rules/reads.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -33,6 +33,7 @@ rule qcreads_paired_il:
         maxqualval=lambda wc: _qcparam(wc, "maxqualval"),
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     conda: "envs/reads.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     shell:
         "( AdapterRemoval"
         "   --file1 {input.reads}"
@@ -68,6 +69,7 @@ rule qcreads_paired_r12:
         maxqualval=lambda wc: _qcparam(wc, "maxqualval"),
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     conda: "envs/reads.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     shell:
         "( AdapterRemoval"
         "   --file1 {input.r1}"
@@ -104,6 +106,7 @@ rule qcreads_se:
         maxqualval=lambda wc: _qcparam(wc, "maxqualval"),
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     conda: "envs/reads.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     shell:
         "( AdapterRemoval"
         "   --file1 {input.se}"
@@ -133,6 +136,7 @@ rule merge_qcd_reads:
         L("reads/runs/{run}~{lib}.fastq.gz.log"),
     resources: **rule_resources(config, "merge_qcd_reads", runtime=30, mem_gb=1, disk_gb=1, cores=1)
     conda: "envs/reads.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     shell:
         "(cat {input} >{output} ) >{log} 2>&1"
 
@@ -145,6 +149,7 @@ rule read_count_librun_indiv:
     log:
         L("stats/reads/readnum_librun/{run}~{lib}.tsv.log"),
     conda: "envs/reads.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     resources: **rule_resources(config, "read_count_librun_indiv", runtime=10, mem_gb=1, disk_gb=1)
     shell:
         "( seqhax stats"
@@ -206,6 +211,7 @@ rule split_pair_sample:
         L("reads/samples/{sample}_split.log"),
     resources: **rule_resources(config, "split_pair_sample", runtime=30, mem_gb=1, disk_gb=1, cores=8)
     conda: "envs/reads.yml"
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     shell:
@@ -236,6 +242,7 @@ rule fastqc_preqc:
         fqczip=P("stats/fastqc/preqc/{run}~{lib}_fastqc.zip"),
     log: L("stats/fastqc/preqc/{run}~{lib}_fastqc.log"),
     resources: **rule_resources(config, "fastqc_preqc", runtime=30, mem_gb=1, cores=1)
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     conda: "envs/qcstats.yml"
     shell:
         "(T=$(mktemp -d);"
@@ -256,6 +263,7 @@ rule fastqc_postqc:
         fqczip=P("stats/fastqc/postqc/{run}~{lib}_fastqc.zip"),
     log: L("stats/fastqc/postqc/{run}~{lib}_fastqc.zip.log"),
     resources: **rule_resources(config, "fastqc_postqc", runtime=30, mem_gb=1, cores=1)
+    container: "docker://ghcr.io/kdm9/acanthophis-qc:latest"
     conda: "envs/qcstats.yml"
     shell:
         "set -x; (T=$(mktemp -d);"
@@ -279,6 +287,7 @@ rule multiqc_fastqc:
         log=L("stats/multiqc/reads-{prepost}~{sampleset}_multiqc.log"),
     resources: **rule_resources(config, "multiqc_fastqc", runtime=30, mem_gb=2)
     conda: "envs/qcstats.yml"
+    container: "docker://multiqc/multiqc:v1.20"
     shell:
         "multiqc"
         "   --no-megaqc-upload"
diff --git a/acanthophis/template/workflow/rules/sampleset.rules b/acanthophis/template/workflow/rules/sampleset.rules
index 8df82b6..8143089 100644
--- a/acanthophis/template/workflow/rules/sampleset.rules
+++ b/acanthophis/template/workflow/rules/sampleset.rules
@@ -1,3 +1,14 @@
+# These rules are part of Acanthophis. See https://github.com/kdm9/Acanthophis.
+# This file *could* be modified, but then be careful when you update them. And
+# please, if you find a bug, raise an issue on github so the fix gets shared
+# with everyone.
+#
+# Copyright 2020-2024 Kevin Murray/Gekkonid Consulting
+#
+# This Source Code Form is subject to the terms of the Mozilla Public License,
+# v. 2.0. If a copy of the MPL was not distributed with this file, You can
+# obtain one at http://mozilla.org/MPL/2.0/.
+
 
 def PL(fns):
     ret = P(fns)
@@ -16,7 +27,7 @@ def all_sampleset_files(wc):
     if config["samplesets"][wc.sampleset].get("varcall", {}).get("snpeff", False):
         print("  - snpeff")
         everything.update(
-                PL(expand("variants/annotated/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}~snpEff.vcf.gz",
+                PL(expand("variants/annotated/{caller}~{aligner}~{ref}~{sampleset}~{filter}~snpEff.vcf.gz",
                  caller=config["samplesets"][wc.sampleset]["varcall"]["callers"],
                  aligner=config["samplesets"][wc.sampleset]["varcall"]["aligners"],
                  ref=config["samplesets"][wc.sampleset]["varcall"]["refs"],
@@ -27,16 +38,24 @@ def all_sampleset_files(wc):
     if "varcall" in config["samplesets"][wc.sampleset]:
         print("  - varcall")
         everything.update(
-               PL(expand("variants/final/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}.{ext}",
+               PL(expand("variants/final/{caller}~{aligner}~{ref}~{sampleset}~{filter}.{ext}",
                       ext=["bcf", "bcf.csi", "vcf.gz", "vcf.gz.csi", "vcf.gz.stats"] if config["tool_settings"].get("varcall", {}).get("make_bcfs", False)
                        else ["vcf.gz", "vcf.gz.csi", "vcf.gz.stats"],
-                      caller=config["samplesets"][wc.sampleset]["varcall"]["callers"],
+                      caller=filter(lambda x: x in ["mpileup", "freebayes"], config["samplesets"][wc.sampleset]["varcall"]["callers"]),
                       aligner=config["samplesets"][wc.sampleset]["varcall"]["aligners"],
                       ref=config["samplesets"][wc.sampleset]["varcall"]["refs"],
                       filter=config["samplesets"][wc.sampleset]["varcall"]["filters"],
                       sampleset=wc.sampleset))
         )
 
+        if "deepvariant" in config["samplesets"][wc.sampleset].get("varcall", {}).get("callers", []):
+            everything.update(
+                TL(expand("deepvariant/{aligner}~{ref}~{sampleset}.vcf.gz",
+                       aligner=config["samplesets"][wc.sampleset]["varcall"]["aligners"],
+                       ref=config["samplesets"][wc.sampleset]["varcall"]["refs"],
+                       sampleset=wc.sampleset))
+            )
+
     if "graftm" in config["samplesets"][wc.sampleset]:
         print("  - graftm")
         everything.update(
@@ -176,6 +195,8 @@ def all_sampleset_files(wc):
                       aligner=config["samplesets"][wc.sampleset].get("align", {}).get("aligners", []),
                       sampleset=wc.sampleset))
         )
+    if config["samplesets"][wc.sampleset].get("align", {}).get("qualimap", False):
+        print("  - qualimap")
         everything.update(
             PL(expand("stats/multiqc/qualimap_{aligner}~{ref}~{sampleset}_multiqc.html",
                        ref=config["samplesets"][wc.sampleset].get("align", {}).get("references", []),
diff --git a/acanthophis/template/workflow/rules/taxonid.rules b/acanthophis/template/workflow/rules/taxonid.rules
index e30bd44..efe414e 100644
--- a/acanthophis/template/workflow/rules/taxonid.rules
+++ b/acanthophis/template/workflow/rules/taxonid.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -26,6 +26,7 @@ rule kraken_noreads:
     log: L("taxonid/kraken/{db}~{sample}.log"),
     benchmark: L("taxonid/kraken/{db}~{sample}.bench.csv"),
     resources: **rule_resources(config, "kraken_noreads", runtime=90, mem_gb=100, disk_gb=24, cores=4)
+    container: "docker://ghcr.io/kdm9/kraken2:latest"
     conda: "envs/kraken.yml"
     params:
         ziplevel=int(config.get("tool_settings", {}).get('ziplevel', 6)) + 2,
@@ -56,6 +57,7 @@ rule kraken_reads:
     benchmark: L("taxonid/kraken/{db}~{sample}.bench.csv"),
     resources: **rule_resources(config, "kraken_reads", runtime=90, mem_gb=100, disk_gb=24, cores=4)
     conda: "envs/kraken.yml"
+    container: "docker://ghcr.io/kdm9/kraken2:latest"
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     shell:
@@ -83,6 +85,7 @@ rule bracken:
     benchmark: L("taxonid/bracken/{db}~{sample}~k{len}.bench.csv"),
     resources: **rule_resources(config, "bracken", runtime=10, mem_gb=20, disk_gb=24, cores=1)
     conda: "envs/kraken.yml"
+    container: "docker://ghcr.io/kdm9/kraken2:latest"
     shell:
         "bracken"
         "   -d {input.db}"
@@ -106,6 +109,7 @@ rule multiqc_kraken:
     log: L("stats/multiqc/kraken_{db}~{sampleset}_multiqc.log"),
     benchmark: L("stats/multiqc/kraken_{db}~{sampleset}_multiqc.bench.csv"),
     conda: "envs/qcstats.yml"
+    container: "docker://multiqc/multiqc:v1.20"
     resources: **rule_resources(config, "multiqc_kraken", runtime=30, mem_gb=2)
     shell:
         "multiqc"
diff --git a/acanthophis/template/workflow/rules/varcall.rules b/acanthophis/template/workflow/rules/varcall.rules
index 2e53622..1f6d717 100644
--- a/acanthophis/template/workflow/rules/varcall.rules
+++ b/acanthophis/template/workflow/rules/varcall.rules
@@ -3,7 +3,7 @@
 # please, if you find a bug, raise an issue on github so the fix gets shared
 # with everyone.
 #
-# Copyright 2016-2022 Kevin Murray/Gekkonid Consulting
+# Copyright 2016-2024 Kevin Murray/Gekkonid Consulting
 #
 # This Source Code Form is subject to the terms of the Mozilla Public License,
 # v. 2.0. If a copy of the MPL was not distributed with this file, You can
@@ -118,6 +118,7 @@ rule mpileup:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     resources: **rule_resources(config, "mpileup", runtime=120, mem_gb=4, cores=1)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     group: "varcall_oneregion"
     shell:
         "( bcftools mpileup"
@@ -168,6 +169,7 @@ rule freebayes:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     resources: **rule_resources(config, "freebayes", runtime=240, mem_gb=8, cores=1)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     shell:
         "( freebayes"
         "   --theta {params.theta}"
@@ -199,14 +201,15 @@ rule bcffilter:
         ref=lambda wc: R(config["data_paths"]["references"][wc.ref]["fasta"], keep_local=True),
     output:
         # Not a pipe! can't run all regions separately if this is a pipe into merge
-        bcf=temp(T("variants/filter_split/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}/{region}.bcf")),
+        bcf=temp(T("variants/filter_split/{caller}~{aligner}~{ref}~{sampleset}~{filter}/{region}.bcf")),
     log:
-        L("variants/filter_split/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}/{region}.bcf.log"),
+        L("variants/filter_split/{caller}~{aligner}~{ref}~{sampleset}~{filter}/{region}.bcf.log"),
     params:
         filtarg=lambda wc: config["tool_settings"]["varcall"]["filters"][wc.filter].replace('\n', ' ')
     group: "varcall_oneregion"
     resources: **rule_resources(config, "bcffilter", runtime=120, mem_gb=4, cores=1)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     shell:
         "( bcftools norm"
         "   --fasta-ref {input.ref}"
@@ -228,13 +231,14 @@ rule bcffilter:
 
 rule premergevariantidx:
     input:
-        T("variants/filter_split/{path}")
+        T("variants/{stage}_split/{path}")
     output:
-        temp(T("variants/filter_split/{path}.csi"))
+        temp(T("variants/{stage}_split/{path}.csi"))
     log:
-        T("variants/filter_split/{path}.csi.log")
+        T("variants/{stage}_split/{path}.csi.log")
     resources: **rule_resources(config, "variantidx", runtime=720, mem_gb=8, cores=1)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     group: "varcall_oneregion"
     shell:
         "bcftools index -f {input}"
@@ -265,7 +269,7 @@ def get_regions(wc, chunked=False):
     regions = []
     with open(regbed) as fh:
         for line in fh:
-            region_chr, region_start, region_stop, _ = line.rstrip("\n").split("\t")
+            region_chr, region_start, region_stop, = line.rstrip("\n").split("\t")[:3]
             region_start = int(region_start) + 1
             regions.append(f"{region_chr}:{region_start}-{region_stop}")
     if chunked:
@@ -275,20 +279,25 @@ def get_regions(wc, chunked=False):
 
 rule bcfmerge2group:
     input:
-        bcf=lambda wc: expand(T("variants/filter_split/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}/{region}.bcf"),
-                    caller=wc.caller, aligner=wc.aligner, ref=wc.ref, sampleset=wc.sampleset, filter=wc.filter,
+        bcf=lambda wc: expand(T("variants/{stage}_split/{caller}~{aligner}~{ref}~{sampleset}{filter}/{region}.bcf"),
+                    caller=wc.caller, aligner=wc.aligner, ref=wc.ref, sampleset=wc.sampleset,
+                    filter=(f"~{wc.filter}" if wc.filter != "raw" else ""),
+                    stage=("filter" if wc.filter != "raw" else "raw"),
                     region=get_regions(wc, chunked=True)[wc.group]),
-        bcfi=lambda wc: expand(T("variants/filter_split/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}/{region}.bcf.csi"),
-                    caller=wc.caller, aligner=wc.aligner, ref=wc.ref, sampleset=wc.sampleset, filter=wc.filter,
+        bcfi=lambda wc: expand(T("variants/{stage}_split/{caller}~{aligner}~{ref}~{sampleset}{filter}/{region}.bcf.csi"),
+                    caller=wc.caller, aligner=wc.aligner, ref=wc.ref, sampleset=wc.sampleset,
+                    filter=(f"~{wc.filter}" if wc.filter != "raw" else ""),
+                    stage=("filter" if wc.filter != "raw" else "raw"),
                     region=get_regions(wc, chunked=True)[wc.group]),
         regbed=lambda wc: config["samplesets"][wc.sampleset].get("varcall", {}).get("region_beds", {}).get(wc.ref, {}).get(wc.caller, [])
     output:
-        bcf=T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}~{group}.bcf"),
-        bcfi=T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}~{group}.bcf.csi"),
+        bcf=T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~{filter}~{group}.bcf"),
+        bcfi=T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~{filter}~{group}.bcf.csi"),
     log:
-        T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}~{group}.bcf.log"),
+        T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~{filter}~{group}.bcf.log"),
     resources: **rule_resources(config, "bcfmerge2group", runtime=1440, mem_gb=12, cores=4)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     params:
     shell:
         "( bcftools concat"
@@ -304,16 +313,17 @@ rule bcfmerge2group:
 
 rule bcfmerge:
     input:
-        bcf=lambda wc: expand(T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}~{group}.bcf"),
+        bcf=lambda wc: expand(T("variants/group_merged/{caller}~{aligner}~{ref}~{sampleset}~{filter}~{group}.bcf"),
                     caller=wc.caller, aligner=wc.aligner, ref=wc.ref, sampleset=wc.sampleset, filter=wc.filter,
                     group=get_regions(wc, chunked=True)),
         regbed=lambda wc: config["samplesets"][wc.sampleset].get("varcall", {}).get("region_beds", {}).get(wc.ref, {}).get(wc.caller, [])
     output:
-        vcf=P("variants/final/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}.vcf.gz"),
+        vcf=P("variants/final/{caller}~{aligner}~{ref}~{sampleset}~{filter}.vcf.gz"),
     log:
-        L("variants/final/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}.vcf.gz.log"),
+        L("variants/final/{caller}~{aligner}~{ref}~{sampleset}~{filter}.vcf.gz.log"),
     resources: **rule_resources(config, "bcfmerge", runtime=1440, mem_gb=12, cores=64)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     shell:
@@ -336,6 +346,7 @@ rule vcfstats:
         P("variants/{path}.vcf.gz.stats")
     log: L("variants/{path}.vcf.gz.stats.log")
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     resources: **rule_resources(config, "vcfstats", runtime=720, mem_gb=4, cores=4)
     shell:
         "bcftools stats -s - -d 0,1000,1 --threads {threads} {input} >{output}"
@@ -352,6 +363,7 @@ rule vcf2bcf:
     log: L("{path}.vcf.gz.log"),
     resources: **rule_resources(config, "vcf2bcf", runtime=720, mem_gb=8, cores=8)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     params:
         ziplevel=config.get("tool_settings", {}).get('ziplevel', 6),
     shell:
@@ -370,6 +382,7 @@ rule finalvarianttbi:
         P("variants/final/{path}.vcf.gz.tbi"),
     resources: **rule_resources(config, "finalvarianttbi", runtime=720, mem_gb=8, cores=1)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     shell:
         "bcftools index -t -f {input}"
 
@@ -381,6 +394,7 @@ rule finalvariantidx:
         P("variants/final/{path}.csi")
     resources: **rule_resources(config, "finalvariantidx", runtime=720, mem_gb=8, cores=1)
     conda: "envs/varcall.yml"
+    container: "docker://ghcr.io/kdm9/varcall:latest"
     shell:
         "bcftools index -f {input}"
 
@@ -390,7 +404,7 @@ rule finalvariantidx:
 #######################################################################
 rule all_filtered_variants:
     input:
-        [P(expand("variants/final/{caller}~{aligner}~{ref}~{sampleset}~filtered-{filter}.{ext}",
+        [P(expand("variants/final/{caller}~{aligner}~{ref}~{sampleset}~{filter}.{ext}",
                ext=["bcf", "bcf.csi", "vcf.gz", "vcf.gz.csi", "vcf.gz.stats"] if config["tool_settings"].get("varcall", {}).get("make_bcfs", False)
                 else ["vcf.gz", "vcf.gz.csi", "vcf.gz.stats"],
                caller=filter(lambda x: x in ["mpileup", "freebayes"], config["samplesets"][sampleset]["varcall"]["callers"]),