Add full HVP metagenomics conda environment

Replaces the placeholder env.yaml with the full pipeline environment
including tools for HiFi alignment, metagenome assembly, binning,
bin QC, taxonomic classification, and viral identification.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: tpshea2

docker/hvp-monolith/env.yaml

@@ -2,22 +2,64 @@ name: base
 channels:
   - conda-forge
   - bioconda
+  - defaults
 dependencies:
-  # QC tools
+  # Read QC & Sequence Utilities
   - fastqc
   - multiqc
+  - seqkit
 
-  # Alignment/BAM tools
+  # PacBio HiFi Alignment
+  - pbmm2          # PacBio-native HiFi read aligner
+  - minimap2        # general-purpose long-read aligner
   - samtools
 
-  # Python and libraries
+  # Metagenome Assembly
+  - hifiasm_meta    # HiFi-specific metagenome assembler
+  - flye            # run with --meta flag for metagenome mode (metaFlye)
+  - metamdbg        # long-read metagenome assembler
+  - myloasm         # metagenomic assembler
+
+  # Binning
+  - metabat2
+  - maxbin2
+  - concoct
+  - semibin         # SemiBin2
+  - das_tool        # DAS Tool - integrates results from multiple binners
+
+  # Bin Quality Assessment
+  - checkm2
+
+  # Genome Comparison / ANI
+  - skani
+
+  # Taxonomic Classification
+  - kraken2
+  - bracken
+  - diamond         # protein-level classification; also a dependency of vConTACT2, CheckM2, VIBRANT, geNomad
+
+  # Viral Identification & Classification
+  - genomad         # viral/plasmid detection (current best-in-class)
+  - checkv          # viral genome completeness assessment
+  - virsorter2
+  - vibrant
+  # NOTE: deepvirfinder - EXCLUDED: requires Python 3.6 + theano=1.0.3 + keras=2.2.4, incompatible with python=3.12.
+  #   Requires a separate dedicated conda environment. Tool is a git-cloned script (not a conda package).
+  #   Already installed at /cil/shed/apps/external/DeepVirFinder/
+  # NOTE: vcontact2 - EXCLUDED: requires Python 3.8, incompatible with python=3.12.
+  #   Working conda environment already installed at /cil/shed/apps/external/vcontact2
+  #   (vcontact2=0.11.3, diamond=2.1.24, mcl, clusterone, python=3.8)
+
+  # Python & Libraries
   - python=3.12
   - biopython
+  - pandas
+  - numpy
   - pysam
   - miniwdl
 
-  # CLI utilities
-  - parallel  # GNU parallel
+  # CLI Utilities
+  - pigz            # parallel gzip
+  - parallel        # GNU parallel
   - jq
-  - pigz
   - zstd