Merge pull request #99 from AndreaGuarracino/patch-2

several fixes in the website, added links to video talk and poster, new pangenome generation workflow

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'
+]