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-rw-r--r--.gitmodules3
-rw-r--r--workflows/pangenome-generate/pangenome-generate.cwl44
m---------workflows/tools0
3 files changed, 47 insertions, 0 deletions
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..c7d7f99
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "workflows/tools"]
+ path = workflows/tools
+ url = https://github.com/common-workflow-library/bio-cwl-tools.git
diff --git a/workflows/pangenome-generate/pangenome-generate.cwl b/workflows/pangenome-generate/pangenome-generate.cwl
index 6794e2d..05e3511 100644
--- a/workflows/pangenome-generate/pangenome-generate.cwl
+++ b/workflows/pangenome-generate/pangenome-generate.cwl
@@ -1,10 +1,22 @@
+#!/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
@@ -24,6 +36,12 @@ outputs:
mergedMetadata:
type: File
outputSource: mergeMetadata/merged
+ indexed_paths:
+ type: File
+ outputSource: index_paths/indexed_paths
+ colinear_components:
+ type: File[]
+ outputSource: segment_components/colinear_components
steps:
relabel:
in:
@@ -66,3 +84,29 @@ 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 ]
diff --git a/workflows/tools b/workflows/tools
new file mode 160000
+Subproject 45c2d6dab199cb931b28c54863924ff3cf9079c