message: Hello world!

threads: 16

pggb_wfmash: true
pggb_fasta:
  class: File
  path: ../data/qc/relabeledSeqs.sorted.qc.100sample.fasta
pggb_mash_k_mer: 19
pggb_map_percent_identity: 95
pggb_num_secondary_mappings: 10000
pggb_segment_length: 5000
pggb_output_dir: "."

odgi_paths: paths
odgi_graph:
  class: File
  path: ./relabeledSeqs.sorted.qc.100sample.fasta.pggb-W-s5000-l15000-p95-n10000-a0-K19-k19-w10000-j5000-e5000-I0-R0.smooth.og
haplotypes: true

consensus_regex: '!/^Consensus/' 
coverage_tsv:
  class: File
  path: ./coverage.tsv

main_py_script:
  class: File
  path: ../main.py
metadata: get-metadata
coverage_matrix:
  class: File
  path: ./coverage.no_consensus.tsv
coverage_matrix_with_metadata: ./coverage.metadata.tsv

clado-rsvd: clado-rsvd
cladogram_matrix:
  class: File
  path: ./coverage.metadata.tsv
reduced_matrix: ./coverage.reduced.tsv
svg_figure: 30k_700cm.svg

newick: gen-newick
newick_dimensions: 100
newick_coverage_matrix:
  class: File
  path: ./coverage.metadata.tsv
newick_metadata: ./metadata.tsv
newick_tree: ./tree.workflow.nwk

nextstrain_R_script:
  class: File
  path: ../taxophages/viz/nextstrain.R 

coverage_matrix_with_metadata_2:
  class: File
  path: ../data/5k/covmatrix.5k.metadata.tsv

metadata_only: ./metadata.tsv
newick_tree: tree.workflow.nwk
distance_matrix: distance_matrix.workflow.tsv
rsvd_dimensions: "1000"
filter_unknowns: "TRUE"

nextstrain_bash_script:
  class: File
  path: ../scripts/nextstrain.sh

newick_tree_2:
  class: File
  path: ./tree.workflow.nwk

metadata_newick:
  class: File
  path: ./metadata.tsv

dataDir: 
  class: Directory
  path: ../config