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authorPeter Amstutz2020-08-19 15:15:57 -0400
committerPeter Amstutz2020-08-19 16:31:38 -0400
commitd1e8809a15ae74d0b847abb80f9f63f53078e1d6 (patch)
tree77a62801b9e8928889d85dadccf1ffce85b2e0cb /workflows/pangenome-generate/pangenome-generate_spoa.cwl
parentb3d2ccf951903ac0b7d717357fb1cccca26fbd15 (diff)
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Scaling pangenome generation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'workflows/pangenome-generate/pangenome-generate_spoa.cwl')
-rw-r--r--workflows/pangenome-generate/pangenome-generate_spoa.cwl110
1 files changed, 61 insertions, 49 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
index 33bf64e..ed12254 100644
--- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -19,9 +19,9 @@ outputs:
odgiGraph:
type: File
outputSource: buildGraph/odgiGraph
- odgiPNG:
- type: File
- outputSource: vizGraph/graph_image
+# odgiPNG:
+# type: File
+# outputSource: vizGraph/graph_image
spoaGFA:
type: File
outputSource: induceGraph/spoaGFA
@@ -34,16 +34,16 @@ outputs:
mergedMetadata:
type: File
outputSource: dups2metadata/merged
- indexed_paths:
- type: File
- outputSource: index_paths/indexed_paths
- colinear_components:
- type: Directory
- outputSource: segment_components/colinear_components
+# indexed_paths:
+# type: File
+# outputSource: index_paths/indexed_paths
+# colinear_components:
+# type: Directory
+# outputSource: segment_components/colinear_components
steps:
dedup_and_sort_by_quality_and_len:
in: {reads: seqs}
- out: [reads_dedupped_sorted_by_quality_and_len, dups]
+ out: [sortedReadsFA, dups]
run: sort_fasta_by_quality_and_len.cwl
induceGraph:
in:
@@ -54,19 +54,23 @@ steps:
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
+ # 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]
+ # requirements:
+ # ResourceRequirement:
+ # ramMin: $(15 * 1024)
+ # outdirMin: 10
+ # run: ../tools/odgi/odgi_viz.cwl
odgi2rdf:
in: {odgi: buildGraph/odgiGraph}
out: [rdf]
@@ -77,29 +81,37 @@ steps:
dups: dedup_and_sort_by_quality_and_len/dups
out: [merged]
run: dups2metadata.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 ]
+ # bin_paths:
+ # requirements:
+ # ResourceRequirement:
+ # ramMin: 3000
+ # outdirMin: 10
+ # 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
+ # requirements:
+ # ResourceRequirement:
+ # ramMin: 3000
+ # outdirMin: 10
+ # 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 ]