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authorPeter Amstutz2020-08-19 15:19:07 -0400
committerPeter Amstutz2020-08-19 16:31:38 -0400
commitb3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch)
tree92adcacbd208546bf3f063e6c25765e660972244 /workflows/pangenome-generate/pangenome-generate_spoa.cwl
parent592c921a3223c03d8a22f7a852641ac5d753fb31 (diff)
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Consolidate steps to scale graph generation workflow
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.cwl25
1 files changed, 6 insertions, 19 deletions
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
index 8b34ff8..33bf64e 100644
--- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -5,11 +5,8 @@ requirements:
ScatterFeatureRequirement: {}
StepInputExpressionRequirement: {}
inputs:
- inputReads: File[]
- metadata: File[]
- metadataSchema: File
- subjects: string[]
- exclude: File?
+ seqs: File
+ metadata: File
bin_widths:
type: int[]
default: [ 1, 4, 16, 64, 256, 1000, 4000, 16000]
@@ -36,7 +33,7 @@ outputs:
outputSource: dedup_and_sort_by_quality_and_len/reads_dedupped_sorted_by_quality_and_len
mergedMetadata:
type: File
- outputSource: mergeMetadata/merged
+ outputSource: dups2metadata/merged
indexed_paths:
type: File
outputSource: index_paths/indexed_paths
@@ -44,15 +41,8 @@ outputs:
type: Directory
outputSource: segment_components/colinear_components
steps:
- relabel:
- in:
- readsFA: inputReads
- subjects: subjects
- exclude: exclude
- out: [relabeledSeqs, originalLabels]
- run: relabel-seqs.cwl
dedup_and_sort_by_quality_and_len:
- in: {reads: relabel/relabeledSeqs}
+ in: {reads: seqs}
out: [reads_dedupped_sorted_by_quality_and_len, dups]
run: sort_fasta_by_quality_and_len.cwl
induceGraph:
@@ -81,15 +71,12 @@ steps:
in: {odgi: buildGraph/odgiGraph}
out: [rdf]
run: odgi_to_rdf.cwl
- mergeMetadata:
+ dups2metadata:
in:
metadata: metadata
- metadataSchema: metadataSchema
- subjects: subjects
dups: dedup_and_sort_by_quality_and_len/dups
- originalLabels: relabel/originalLabels
out: [merged]
- run: merge-metadata.cwl
+ run: dups2metadata.cwl
bin_paths:
run: ../tools/odgi/odgi_bin.cwl
in: