added workflow to sort a multifasta by quality and length, and added the overall new pangenome generation workflow with SPOA

1 files changed, 122 insertions, 0 deletions

diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
new file mode 100644
index 0000000..958ffb6
--- /dev/null
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -0,0 +1,122 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: Workflow
+requirements:
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+inputs:
+  inputReads: File[]
+  metadata: File[]
+  metadataSchema: File
+  subjects: string[]
+  exclude: File?
+  bin_widths:
+    type: int[]
+    default: [ 1, 4, 16, 64, 256, 1000, 4000, 16000]
+    doc: width of each bin in basepairs along the graph vector
+  cells_per_file:
+    type: int
+    default: 100
+    doc: Cells per file on component_segmentation
+outputs:
+  odgiGraph:
+    type: File
+    outputSource: buildGraph/odgiGraph
+  odgiPNG:
+    type: File
+    outputSource: vizGraph/graph_image
+  spoaGFA:
+    type: File
+    outputSource: induceGraph/spoaGFA
+  odgiRDF:
+    type: File
+    outputSource: odgi2rdf/rdf
+  readsMergeDedup:
+    type: File
+    outputSource: dedup/reads_dedup
+  mergedMetadata:
+    type: File
+    outputSource: mergeMetadata/merged
+  indexed_paths:
+    type: File
+    outputSource: index_paths/indexed_paths
+  colinear_components:
+    type: Directory
+    outputSource: segment_components/colinear_components
+steps:
+  relabel:
+    in:
+      readsFA: inputReads
+      subjects: subjects
+      exclude: exclude
+    out: [relabeledSeqs, originalLabels]
+    run: relabel-seqs.cwl
+  dedup:
+    in: {reads: relabel/relabeledSeqs}
+    out: [reads_dedup, dups]
+    run: ../tools/seqkit/seqkit_rmdup.cwl
+  sort_by_quality_and_len:
+    in: {reads: dedup/reads_dedup}
+    out: [reads_sorted_by_quality_and_len]
+    run: sort_fasta_by_quality_and_len.cwl
+  induceGraph:
+    in:
+      readsFA: sort_by_quality_and_len/reads_sorted_by_quality_and_len
+    out: [spoaGFA]
+    run: spoa.cwl
+  buildGraph:
+    in: {inputGFA: induceGraph/spoaGFA}
+    out: [odgiGraph]
+    run: odgi-build-from-spoa-gfa.cwl
+  vizGraph:
+    in:
+      sparse_graph_index: buildGraph/odgiGraph
+      width:
+        default: 50000
+      height:
+        default: 500
+      path_per_row:
+        default: true
+      path_height:
+        default: 4
+    out: [graph_image]
+    run: ../tools/odgi/odgi_viz.cwl
+  odgi2rdf:
+    in: {odgi: buildGraph/odgiGraph}
+    out: [rdf]
+    run: odgi_to_rdf.cwl
+  mergeMetadata:
+    in:
+      metadata: metadata
+      metadataSchema: metadataSchema
+      subjects: subjects
+      dups: dedup/dups
+      originalLabels: relabel/originalLabels
+    out: [merged]
+    run: merge-metadata.cwl
+  bin_paths:
+    run: ../tools/odgi/odgi_bin.cwl
+    in:
+      sparse_graph_index: buildGraph/odgiGraph
+      bin_width: bin_widths
+    scatter: bin_width
+    out: [ bins, pangenome_sequence ]
+  index_paths:
+    label: Create path index
+    run: ../tools/odgi/odgi_pathindex.cwl
+    in:
+      sparse_graph_index: buildGraph/odgiGraph
+    out: [ indexed_paths ]
+  segment_components:
+    label: Run component segmentation
+    run: ../tools/graph-genome-segmentation/component_segmentation.cwl
+    in:
+      bins: bin_paths/bins
+      cells_per_file: cells_per_file
+      pangenome_sequence:
+        source: bin_paths/pangenome_sequence
+        valueFrom: $(self[0])
+        # the bin_paths step is scattered over the bin_width array, but always using the same sparse_graph_index
+        # the pangenome_sequence that is extracted is exactly the same for the same sparse_graph_index
+        # regardless of bin_width, so we take the first pangenome_sequence as input for this step
+    out: [ colinear_components ]