1 files changed, 118 insertions, 0 deletions
diff --git a/workflows/phylogeny/phylogeny.cwl b/workflows/phylogeny/phylogeny.cwl
new file mode 100644
index 0000000..7ae3ab7
--- /dev/null
+++ b/workflows/phylogeny/phylogeny.cwl
@@ -0,0 +1,118 @@
+#!/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]