Merge pull request #49 from mr-c/add_pangenome_browser_prep

add pangenome browser prep

1 files changed, 70 insertions, 13 deletions

diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 6794e2d..1d49904 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -1,17 +1,29 @@
+#!/usr/bin/env cwl-runner
 cwlVersion: v1.1
 class: Workflow
+requirements:
+  ScatterFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
 inputs:
   inputReads: File[]
   metadata: File[]
   metadataSchema: File
   subjects: string[]
+  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/odgiPNG
+    outputSource: vizGraph/graph_image
   seqwishGFA:
     type: File
     outputSource: induceGraph/seqwishGFA
@@ -20,10 +32,16 @@ outputs:
     outputSource: odgi2rdf/rdf
   readsMergeDedup:
     type: File
-    outputSource: dedup/readsMergeDedup
+    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:
@@ -32,17 +50,21 @@ steps:
     out: [relabeledSeqs, originalLabels]
     run: relabel-seqs.cwl
   dedup:
-    in: {readsFA: relabel/relabeledSeqs}
-    out: [readsMergeDedup, dups]
-    run: seqkit-rmdup.cwl
+    in: {reads: relabel/relabeledSeqs}
+    out: [reads_dedup, dups]
+    run: ../tools/seqkit/seqkit_rmdup.cwl
   overlapReads:
-    in: {readsFA: dedup/readsMergeDedup}
-    out: [readsPAF]
-    run: minimap2.cwl
+    in:
+      target: dedup/reads_dedup
+      query: dedup/reads_dedup
+      outputCIGAR:
+        default: true
+    out: [alignments]
+    run: ../tools/minimap2/minimap2_paf.cwl
   induceGraph:
     in:
-      readsFA: dedup/readsMergeDedup
-      readsPAF: overlapReads/readsPAF
+      readsFA: dedup/reads_dedup
+      readsPAF: overlapReads/alignments
     out: [seqwishGFA]
     run: seqwish.cwl
   buildGraph:
@@ -50,9 +72,18 @@ steps:
     out: [odgiGraph]
     run: odgi-build.cwl
   vizGraph:
-    in: {inputODGI: buildGraph/odgiGraph}
-    out: [odgiPNG]
-    run: odgi-viz.cwl
+    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]
@@ -66,3 +97,29 @@ steps:
       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 ]