Merge pull request #117 from arvados/pangenome_workflow_abpoa

Pangenome workflow with abPOA

7 files changed, 168 insertions, 9 deletions

diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py
index eebd9aa..35f61a5 100644
--- a/scripts/create_sra_metadata/create_sra_metadata.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -232,7 +232,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
     taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text
     info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_" + taxon_id
 
-    # This script download and prepare data and metadata for samples that will be mapepd againg a referenceT
+    # This script download and prepare data and metadata for samples that will be mapped against a referenceT
     info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0002028'
 
     EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT')
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..c61e51a
--- /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: "false"
+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 b623054..fa16809 100644
--- a/workflows/pangenome-generate/pangenome-generate_spoa.cwl
+++ b/workflows/pangenome-generate/pangenome-generate_spoa.cwl
@@ -15,6 +15,9 @@ inputs:
     type: int
     default: 100
     doc: Cells per file on component_segmentation
+  reversed_sort:
+    type: string
+    default: "true"
 outputs:
   odgiGraph:
     type: File
@@ -42,7 +45,7 @@ outputs:
 #    outputSource: segment_components/colinear_components
 steps:
   dedup_and_sort_by_quality_and_len:
-    in: {readsFA: seqs}
+    in: {readsFA: seqs, reversed_sorting: reversed_sort}
     out: [sortedReadsFA, dups]
     run: sort_fasta_by_quality_and_len.cwl
   induceGraph:
@@ -53,7 +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
diff --git a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
index 26c20e8..6f71d92 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.cwl
@@ -1,3 +1,4 @@
+
 cwlVersion: v1.1
 class: CommandLineTool
 hints:
@@ -5,6 +6,9 @@ hints:
     coresMin: 1
     ramMin: 3000
 inputs:
+  reversed_sorting:
+    type: string
+    inputBinding: {position: 3}
   readsFA:
     type: File
     inputBinding: {position: 2}
@@ -23,3 +27,4 @@ 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
index e836654..02ebf60 100644
--- a/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
+++ b/workflows/pangenome-generate/sort_fasta_by_quality_and_len.py
@@ -7,15 +7,17 @@ import os
 import sys
 import gzip
 
-#import xxhash # Faster library
+# import xxhash # Faster library
 import hashlib
 
+
 def open_gzipsafe(path_file):
     if path_file.endswith('.gz'):
-    	return gzip.open(path_file, 'rt')
+        return gzip.open(path_file, 'rt')
     else:
         return open(path_file)
 
+
 path_fasta = sys.argv[1]
 
 hash_to_count_and_headers_dict = {}
@@ -28,7 +30,7 @@ with open_gzipsafe(path_fasta) as f:
         header = fasta.strip('\n').split('\n')[0]
         sequence = ''.join(fasta.strip('\n').split('\n')[1:])
 
-        ##hash = xxhash.xxh64(sequence).hexdigest() # Faster library
+        # hash = xxhash.xxh64(sequence).hexdigest() # Faster library
         hash = hashlib.md5(sequence.encode('utf-8')).hexdigest()
 
         if hash not in hash_to_count_and_headers_dict:
@@ -38,15 +40,18 @@ with open_gzipsafe(path_fasta) as f:
             header_to_seq_dict[header] = sequence
 
             seq_len = len(sequence)
-            header_percCalledBases_seqLength_list.append([header, (seq_len - sequence.count('N'))/seq_len, seq_len])
+            header_percCalledBases_seqLength_list.append([header, (seq_len - sequence.count('N')) / seq_len, seq_len])
 
         hash_to_count_and_headers_dict[hash][0] += 1
         hash_to_count_and_headers_dict[hash][1].append(header)
 
-
 with open('dups.txt', 'w') as fw:
     for count, header_list in hash_to_count_and_headers_dict.values():
         fw.write('\t'.join([str(count), ', '.join(header_list)]) + '\n')
 
-for header, percCalledBases, seqLength_list in sorted(header_percCalledBases_seqLength_list, key=lambda x: (x[-2], x[-1]), reverse = True):
+reversed_sorting = True if len(sys.argv) > 2 and sys.argv[2].lower() == 'true' else False
+
+for header, percCalledBases, seqLength_list in sorted(
+        header_percCalledBases_seqLength_list, key=lambda x: (x[-2], x[-1]), reverse=reversed_sorting
+):
     sys.stdout.write('>{}\n{}\n'.format(header, header_to_seq_dict[header]))