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author | AndreaGuarracino | 2020-11-21 23:06:05 +0100 |
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committer | AndreaGuarracino | 2020-11-21 23:06:05 +0100 |
commit | 1e9a735e84a8e89099b1de2ec66c56669caf6cc8 (patch) | |
tree | 0beefb8e9f7a6321a5c8382b1be7b5b809c87d5e /workflows/pangenome-generate | |
parent | 862ae0235e3d1b105fa342cedf4aa59ae73d90c4 (diff) | |
download | bh20-seq-resource-1e9a735e84a8e89099b1de2ec66c56669caf6cc8.tar.gz bh20-seq-resource-1e9a735e84a8e89099b1de2ec66c56669caf6cc8.tar.lz bh20-seq-resource-1e9a735e84a8e89099b1de2ec66c56669caf6cc8.zip |
added abPOA workflow; typos
Diffstat (limited to 'workflows/pangenome-generate')
-rw-r--r-- | workflows/pangenome-generate/abpoa.cwl | 26 | ||||
-rw-r--r-- | workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl (renamed from workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl) | 0 | ||||
-rw-r--r-- | workflows/pangenome-generate/pangenome-generate_abpoa.cwl | 120 | ||||
-rw-r--r-- | workflows/pangenome-generate/pangenome-generate_spoa.cwl | 2 |
4 files changed, 147 insertions, 1 deletions
diff --git a/workflows/pangenome-generate/abpoa.cwl b/workflows/pangenome-generate/abpoa.cwl new file mode 100644 index 0000000..fa9f157 --- /dev/null +++ b/workflows/pangenome-generate/abpoa.cwl @@ -0,0 +1,26 @@ +cwlVersion: v1.1 +class: CommandLineTool +inputs: + readsFA: File + script: + type: File + default: {class: File, location: relabel-seqs.py} +outputs: + abpoaGFA: + type: stdout +requirements: + InlineJavascriptRequirement: {} +hints: + DockerRequirement: + dockerPull: "quay.io/biocontainers/abpoa:1.0.5--hed695b0_0" + ResourceRequirement: + coresMin: 1 + ramMin: $(15 * 1024) + outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20)) +baseCommand: abpoa +stdout: $(inputs.readsFA.nameroot).O0.gfa +arguments: [ + $(inputs.readsFA), + -r 3, + -O, '0' +] diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl index eee4031..eee4031 100644 --- a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl +++ b/workflows/pangenome-generate/odgi-build-from-xpoa-gfa.cwl diff --git a/workflows/pangenome-generate/pangenome-generate_abpoa.cwl b/workflows/pangenome-generate/pangenome-generate_abpoa.cwl new file mode 100644 index 0000000..8f98dc6 --- /dev/null +++ b/workflows/pangenome-generate/pangenome-generate_abpoa.cwl @@ -0,0 +1,120 @@ +#!/usr/bin/env cwl-runner +cwlVersion: v1.1 +class: Workflow +requirements: + ScatterFeatureRequirement: {} + StepInputExpressionRequirement: {} +inputs: + seqs: File + metadata: File + 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 + reversed_sort: + type: string + default: "true" +outputs: + odgiGraph: + type: File + outputSource: buildGraph/odgiGraph + odgiPNG: + type: File + outputSource: vizGraph/graph_image + abpoaGFA: + type: File + outputSource: induceGraph/abpoaGFA +# odgiRDF: +# type: File +# outputSource: odgi2rdf/rdf + readsMergeDedupSortedByQualAndLen: + type: File + outputSource: dedup_and_sort_by_quality_and_len/sortedReadsFA + mergedMetadata: + type: File + outputSource: dups2metadata/merged +# 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: {readsFA: seqs, reversed_sorting: reversed_sort} + out: [sortedReadsFA, dups] + run: sort_fasta_by_quality_and_len.cwl + induceGraph: + in: + readsFA: dedup_and_sort_by_quality_and_len/sortedReadsFA + out: [abpoaGFA] + run: abpoa.cwl + buildGraph: + in: {inputGFA: induceGraph/abpoaGFA} + out: [odgiGraph] + run: odgi-build-from-xpoa-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] + requirements: + ResourceRequirement: + ramMin: $(15 * 1024) + outdirMin: 10 + run: ../tools/odgi/odgi_viz.cwl + # odgi2rdf: + # in: {odgi: buildGraph/odgiGraph} + # out: [rdf] + # run: odgi_to_rdf.cwl + dups2metadata: + in: + metadata: metadata + dups: dedup_and_sort_by_quality_and_len/dups + out: [merged] + run: dups2metadata.cwl + # 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 ] diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl index 4e7302d..fa16809 100644 --- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl +++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl @@ -56,7 +56,7 @@ steps: buildGraph: in: {inputGFA: induceGraph/spoaGFA} out: [odgiGraph] - run: odgi-build-from-spoa-gfa.cwl + run: odgi-build-from-xpoa-gfa.cwl vizGraph: in: sparse_graph_index: buildGraph/odgiGraph |