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authorPeter Amstutz2020-08-05 16:06:11 -0400
committerGitHub2020-08-05 16:06:11 -0400
commitfdb1b012fc04ee07f401541e181e28fe442c9454 (patch)
tree8486db1087692dffcea9d93814e436d9cf150b47 /workflows/pangenome-generate
parent86f31ef60f65a820bf9ac25c3fc01c88f2a9ebfe (diff)
parent2d20bf90497588a297ca98a78ee0fbbcadf95569 (diff)
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Merge pull request #99 from AndreaGuarracino/patch-2
several fixes in the website, added links to video talk and poster, new pangenome generation workflow
Diffstat (limited to 'workflows/pangenome-generate')
-rw-r--r--workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl29
-rw-r--r--workflows/pangenome-generate/pangenome-generate_spoa.cwl122
-rw-r--r--workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl18
-rw-r--r--workflows/pangenome-generate/sort_fasta_by_quality_and_len.py35
-rw-r--r--workflows/pangenome-generate/spoa.cwl27
5 files changed, 231 insertions, 0 deletions
diff --git a/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl
new file mode 100644
index 0000000..2459ce7
--- /dev/null
+++ b/workflows/pangenome-generate/odgi-build-from-spoa-gfa.cwl
@@ -0,0 +1,29 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+ inputGFA: File
+outputs:
+ odgiGraph:
+ type: File
+ outputBinding:
+ glob: $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+requirements:
+ InlineJavascriptRequirement: {}
+ ShellCommandRequirement: {}
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/odgi:v0.3--py37h8b12597_0"
+ ResourceRequirement:
+ coresMin: 4
+ ramMin: $(7 * 1024)
+ outdirMin: $(Math.ceil((inputs.inputGFA.size/(1024*1024*1024)+1) * 2))
+ InitialWorkDirRequirement:
+ listing:
+ - entry: $(inputs.inputGFA)
+ writable: true
+arguments: [odgi, build, -g, $(inputs.inputGFA), -o, -,
+ {shellQuote: false, valueFrom: "|"},
+ odgi, unchop, -i, -, -o, -,
+ {shellQuote: false, valueFrom: "|"},
+ odgi, sort, -i, -, -p, s, -o, $(inputs.inputGFA.nameroot).unchop.sorted.odgi
+ ]
diff --git a/workflows/pangenome-generate/pangenome-generate_spoa.cwl b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
new file mode 100644
index 0000000..958ffb6
--- /dev/null
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -0,0 +1,122 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.1
+class: Workflow
+requirements:
+ ScatterFeatureRequirement: {}
+ StepInputExpressionRequirement: {}
+inputs:
+ inputReads: File[]
+ metadata: File[]
+ metadataSchema: File
+ subjects: string[]
+ exclude: 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
+outputs:
+ odgiGraph:
+ type: File
+ outputSource: buildGraph/odgiGraph
+ odgiPNG:
+ type: File
+ outputSource: vizGraph/graph_image
+ spoaGFA:
+ type: File
+ outputSource: induceGraph/spoaGFA
+ odgiRDF:
+ type: File
+ outputSource: odgi2rdf/rdf
+ readsMergeDedup:
+ type: File
+ outputSource: dedup/reads_dedup
+ mergedMetadata:
+ type: File
+ outputSource: mergeMetadata/merged
+ indexed_paths:
+ type: File
+ outputSource: index_paths/indexed_paths
+ colinear_components:
+ type: Directory
+ outputSource: segment_components/colinear_components
+steps:
+ relabel:
+ in:
+ readsFA: inputReads
+ subjects: subjects
+ exclude: exclude
+ out: [relabeledSeqs, originalLabels]
+ run: relabel-seqs.cwl
+ dedup:
+ in: {reads: relabel/relabeledSeqs}
+ out: [reads_dedup, dups]
+ run: ../tools/seqkit/seqkit_rmdup.cwl
+ sort_by_quality_and_len:
+ in: {reads: dedup/reads_dedup}
+ out: [reads_sorted_by_quality_and_len]
+ run: sort_fasta_by_quality_and_len.cwl
+ induceGraph:
+ in:
+ readsFA: sort_by_quality_and_len/reads_sorted_by_quality_and_len
+ out: [spoaGFA]
+ run: spoa.cwl
+ buildGraph:
+ 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
+ odgi2rdf:
+ in: {odgi: buildGraph/odgiGraph}
+ out: [rdf]
+ run: odgi_to_rdf.cwl
+ mergeMetadata:
+ in:
+ metadata: metadata
+ metadataSchema: metadataSchema
+ subjects: subjects
+ dups: dedup/dups
+ 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/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
new file mode 100644
index 0000000..59f027e
--- /dev/null
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -0,0 +1,18 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+ readsFA:
+ type: File
+ inputBinding: {position: 2}
+ script:
+ type: File
+ inputBinding: {position: 1}
+ default: {class: File, location: sort_fasta_by_quality_and_len.py}
+stdout: $(inputs.readsFA.nameroot).sorted_by_quality_and_len.fasta
+outputs:
+ sortedReadsFA:
+ type: stdout
+requirements:
+ InlineJavascriptRequirement: {}
+ ShellCommandRequirement: {}
+baseCommand: [python]
diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
new file mode 100644
index 0000000..e48fd68
--- /dev/null
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python3
+
+# Sort the sequences by quality (percentage of number of N bases not called, descending) and by length (descending).
+# The best sequence is the longest one, with no uncalled bases.
+
+import os
+import sys
+import gzip
+
+def open_gzipsafe(path_file):
+ if path_file.endswith('.gz'):
+ return gzip.open(path_file, 'rt')
+ else:
+ return open(path_file)
+
+path_fasta = sys.argv[1]
+
+header_to_seq_dict = {}
+header_percCalledBases_seqLength_list = []
+
+with open_gzipsafe(path_fasta) as f:
+ for fasta in f.read().strip('\n>').split('>'):
+ header = fasta.strip('\n').split('\n')[0]
+
+ header_to_seq_dict[
+ header
+ ] = ''.join(fasta.strip('\n').split('\n')[1:])
+
+ seq_len = len(header_to_seq_dict[header])
+ header_percCalledBases_seqLength_list.append([
+ header, header_to_seq_dict[header].count('N'), (seq_len - header_to_seq_dict[header].count('N'))/seq_len, seq_len
+ ])
+
+for header, x, percCalledBases, seqLength_list in sorted(header_percCalledBases_seqLength_list, key=lambda x: (x[-2], x[-1]), reverse = True):
+ sys.stdout.write('>{}\n{}\n'.format(header, header_to_seq_dict[header]))
diff --git a/workflows/pangenome-generate/spoa.cwl b/workflows/pangenome-generate/spoa.cwl
new file mode 100644
index 0000000..1e390d8
--- /dev/null
+++ b/workflows/pangenome-generate/spoa.cwl
@@ -0,0 +1,27 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+ readsFA: File
+stdout: $(inputs.readsFA.nameroot).g6.gfa
+script:
+ type: File
+ default: {class: File, location: relabel-seqs.py}
+outputs:
+ spoaGFA:
+ type: stdout
+requirements:
+ InlineJavascriptRequirement: {}
+ ShellCommandRequirement: {}
+hints:
+ DockerRequirement:
+ dockerPull: "quay.io/biocontainers/spoa:3.0.2--hc9558a2_0"
+ ResourceRequirement:
+ coresMin: 1
+ ramMin: $(15 * 1024)
+ outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
+baseCommand: spoa
+arguments: [
+ $(inputs.readsFA),
+ -G,
+ -g, '-6'
+]