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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
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