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#!/usr/bin/env cwl-runner
cwlVersion: v1.1
class: Workflow
#############################################
inputs:
# align
threads: int
pggb_wfmash: boolean
pggb_fasta: File
pggb_mash_k_mer: int
pggb_map_percent_identity: int
pggb_num_secondary_mappings: int
pggb_segment_length: int
pggb_output_dir: string
# extract coverage vector
odgi_paths: string
odgi_graph: File
haplotypes: boolean
threads: int
# remove consensus paths
consensus_regex: string
coverage_tsv: File
# Get metadata
main_py_script: File
metadata: string
coverage_matrix: File
coverage_matrix_with_metadata: string
# Generate newick tree
main_py_script: File
newick: string
newick_dimensions: int
newick_coverage_matrix: File
newick_metadata: string
newick_tree: string
# Genenrate augur JSON file
nextstrain_bash_script: File
newick_tree_2: File
metadata_newick: File
dataDir: Directory
#############################################
outputs:
augur_json:
type: File
outputSource: augur/newick_json
#############################################
steps:
align:
run: align.cwl
in:
threads: threads
pggb_wfmash: pggb_wfmash
pggb_fasta: pggb_fasta
pggb_mash_k_mer: pggb_mash_k_mer
pggb_map_percent_identity: pggb_map_percent_identity
pggb_num_secondary_mappings: pggb_num_secondary_mappings
pggb_segment_length: pggb_segment_length
pggb_output_dir: pggb_output_dir
out: [pggb_odgi_graph]
odgi:
run: coverage.cwl
in:
odgi_paths: odgi_paths
odgi_graph: align/pggb_odgi_graph
haplotypes: haplotypes
threads: threads
out: [coverage_matrix]
awk:
run: awk-coverage.cwl
in:
consensus_regex: consensus_regex
coverage_tsv: odgi/coverage_matrix
out: [awk_coverage_matrix]
metadata:
run: metadata.cwl
in:
main_py_script: main_py_script
metadata: metadata
coverage_matrix: awk/awk_coverage_matrix
coverage_matrix_with_metadata: coverage_matrix_with_metadata
out: [coverage_matrix_with_metadata_out]
newick:
run: newick.cwl
in:
main_py_script: main_py_script
newick: newick
newick_dimensions: newick_dimensions
newick_coverage_matrix: metadata/coverage_matrix_with_metadata_out
newick_metadata: newick_metadata
newick_tree: newick_tree
out: [metadata_out, newick_tree_out]
augur:
run: augur.cwl
in:
nextstrain_bash_script: nextstrain_bash_script
newick_tree_2: newick/newick_tree_out
metadata_newick: newick/metadata_out
dataDir: dataDir
out: [newick_json]
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