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| author | Peter Amstutz | 2020-08-19 15:19:07 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-08-19 16:31:38 -0400 |
| commit | b3d2ccf951903ac0b7d717357fb1cccca26fbd15 (patch) | |
| tree | 92adcacbd208546bf3f063e6c25765e660972244 /workflows/pangenome-generate/pangenome-generate_spoa.cwl | |
| parent | 592c921a3223c03d8a22f7a852641ac5d753fb31 (diff) | |
| download | bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.gz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.tar.lz bh20-seq-resource-b3d2ccf951903ac0b7d717357fb1cccca26fbd15.zip | |
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.cwl | 25 |
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: |