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authorPjotr Prins2021-01-26 16:22:19 +0000
committerGitHub2021-01-26 16:22:19 +0000
commita54122023ef2bde4ef4fc39355b3491678bbf773 (patch)
tree150bef4a574486db9e7c16d87be89ad219d84bb1 /workflows/phylogeny/phylogeny.cwl
parentb112b3203e34ea61dfdf802bce5036f938eaa774 (diff)
parent4842117f530aba08b4a253aee533a8d4802b1c12 (diff)
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Merge pull request #124 from urbanslug/master
Add phylogeny workflow
Diffstat (limited to 'workflows/phylogeny/phylogeny.cwl')
-rw-r--r--workflows/phylogeny/phylogeny.cwl118
1 files changed, 118 insertions, 0 deletions
diff --git a/workflows/phylogeny/phylogeny.cwl b/workflows/phylogeny/phylogeny.cwl
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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]