MetaInformAnt/config/amalgkit/amalgkit_temnothorax_nylanderi.yaml at main · docxology/MetaInformAnt · GitHub

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# METAINFORMANT Amalgkit Configuration
# Species: Temnothorax nylanderi
# NCBI Taxonomy ID: 102681
# Assembly: GCF_030848795.1 (tnyl_v1.0)
# Assembly Level: Contig
# Sequencing: N/A
# Annotation: GCF_030848795.1-RS_2025_02
# Annotation Release: RS_2025_02
# Notes: European acorn ant, social immunity research
# RNA-seq Samples Available: 166
# Generated: 2026-02-09

# Paths are resolved relative to repository root
work_dir: output/amalgkit/temnothorax_nylanderi/work
log_dir: output/amalgkit/temnothorax_nylanderi/logs
threads: 16

auto_install_amalgkit: true

# Pre-selection filtering rules
filters:
  require_tissue: false

# Species configuration
species_list:
  - Temnothorax_nylanderi

taxon_id: 102681

# Reference genome configuration — shared genome directory
genome:
  accession: GCF_030848795.1
  assembly_name: tnyl_v1.0
  annotation_release: RS_2025_02
  dest_dir: output/amalgkit/shared/genome/Temnothorax_nylanderi
  include:
    - genome
    - gff3
    - rna
    - cds
    - protein
  ftp_url: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/030/848/795/GCF_030848795.1_tnyl_v1.0/
  files:
    genomic_fasta: GCF_030848795.1_tnyl_v1.0_genomic.fna.gz
    transcriptome_fasta: GCF_030848795.1_tnyl_v1.0_rna_from_genomic.fna.gz
    cds_fasta: GCF_030848795.1_tnyl_v1.0_cds_from_genomic.fna.gz
    protein_fasta: GCF_030848795.1_tnyl_v1.0_protein.faa.gz
    annotation_gff: GCF_030848795.1_tnyl_v1.0_genomic.gff.gz

# Per-step parameters
steps:
  metadata:
    out_dir: output/amalgkit/temnothorax_nylanderi/work
    search_string: '"Temnothorax nylanderi"[Organism] AND "RNA-Seq"[Strategy] AND "Illumina"[Platform]'
    redo: no
  integrate:
    fastq_dir: output/amalgkit/temnothorax_nylanderi/fastq/getfastq
  select:
    select_rules_tsv: config/amalgkit/select_rules.tsv
  getfastq:
    out_dir: output/amalgkit/temnothorax_nylanderi/fastq
    threads: 16
    redo: no
    aws: yes
    gcp: no
    ncbi: no
    fastp: no
    max_bp: 50000000
  quant:
    out_dir: output/amalgkit/temnothorax_nylanderi/work
    threads: 16
    redo: no
    build_index: no
    clean_fastq: no
    index_dir: output/amalgkit/shared/genome/Temnothorax_nylanderi/index
    fasta_dir: output/amalgkit/shared/genome/Temnothorax_nylanderi
  merge:
    out_dir: output/amalgkit/temnothorax_nylanderi/work
  wsfilter:
    out_dir: output/amalgkit/temnothorax_nylanderi/work
    input_dir: output/amalgkit/temnothorax_nylanderi/work/merge
    norm: log2p1-fpkm
    mapping_rate: 0.2
  finalize:
    out_dir: output/amalgkit/temnothorax_nylanderi/work
    input_dir: output/amalgkit/temnothorax_nylanderi/work/wsfilter
    norm: log2p1-fpkm
    batch_effect_alg: no
  sanity: {}