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-rw-r--r--workflows/pangenome-generate/merge-metadata.cwl46
-rw-r--r--workflows/pangenome-generate/merge-metadata.py33
-rw-r--r--workflows/pangenome-generate/minimap2.cwl2
-rw-r--r--workflows/pangenome-generate/relabel-seqs.cwl33
-rw-r--r--workflows/pangenome-generate/relabel-seqs.py24
5 files changed, 110 insertions, 28 deletions
diff --git a/workflows/pangenome-generate/merge-metadata.cwl b/workflows/pangenome-generate/merge-metadata.cwl
index fcefe32..4d9c808 100644
--- a/workflows/pangenome-generate/merge-metadata.cwl
+++ b/workflows/pangenome-generate/merge-metadata.cwl
@@ -5,16 +5,48 @@ hints:
dockerPull: commonworkflowlanguage/cwltool_module
inputs:
metadata: File[]
- metadataSchema: File
subjects: string[]
- dups: File?
- originalLabels: File
+ metadataSchema:
+ type: File
+ inputBinding: {position: 2}
+ originalLabels:
+ type: File
+ inputBinding: {position: 3}
+ dups:
+ type: File?
+ inputBinding: {position: 4}
+ script:
+ type: File
+ inputBinding: {position: 1}
+ default: {class: File, location: merge-metadata.py}
outputs:
merged: stdout
stdout: mergedmetadata.ttl
requirements:
+ InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
- listing:
- - entry: {$include: merge-metadata.py}
- entryname: merge-metadata.py
-baseCommand: [python3, merge-metadata.py]
+ listing: |
+ ${
+ var i = 0;
+ var b = 1;
+ var out = [];
+ for (; i < inputs.metadata.length; i++) {
+ var block = [];
+ var sub = [];
+ for (; i < (b*150) && i < inputs.metadata.length; i++) {
+ block.push(inputs.metadata[i]);
+ sub.push(inputs.subjects[i]);
+ }
+ out.push({
+ entryname: "block"+b,
+ entry: JSON.stringify(block)
+ });
+ out.push({
+ entryname: "subs"+b,
+ entry: JSON.stringify(sub)
+ });
+ b++;
+ }
+ return out;
+ }
+baseCommand: python
diff --git a/workflows/pangenome-generate/merge-metadata.py b/workflows/pangenome-generate/merge-metadata.py
index bfec781..65d08a6 100644
--- a/workflows/pangenome-generate/merge-metadata.py
+++ b/workflows/pangenome-generate/merge-metadata.py
@@ -2,12 +2,27 @@ import re
import schema_salad.schema
import schema_salad.jsonld_context
import json
+import sys
+import os
+import logging
+
+metadataSchema = sys.argv[1]
+originalLabels = sys.argv[2]
+dups = None
+if len(sys.argv) == 4:
+ dups = sys.argv[3]
+
+def readitems(stem):
+ items = []
+ b = 1
+ while os.path.exists("%s%i" % (stem, b)):
+ with open("%s%i" % (stem, b)) as f:
+ items.extend(json.load(f))
+ b += 1
+ return items
-metadataSchema = '$(inputs.metadataSchema.path)'
-metadata = $(inputs.metadata)
-subjects = $(inputs.subjects)
-dups = json.loads('''$(inputs.dups)''')
-originalLabels = $(inputs.originalLabels)
+metadata = readitems("block")
+subjects = readitems("subs")
(document_loader,
avsc_names,
@@ -20,17 +35,15 @@ for i, m in enumerate(metadata):
g = schema_salad.jsonld_context.makerdf(subjects[i], doc, document_loader.ctx)
print(g.serialize(format="ntriples").decode("utf-8"))
-import logging
-
if dups:
- sameseqs = open(dups["path"], "rt")
+ sameseqs = open(dups, "rt")
for d in sameseqs:
logging.warn(d)
- g = re.match(r"\\d+\\t(.*)", d)
+ g = re.match(r"\d+\t(.*)", d)
logging.warn("%s", g.group(1))
sp = g.group(1).split(",")
for n in sp[1:]:
print("<%s> <http://biohackathon.org/bh20-seq-schema/has_duplicate_sequence> <%s> ." % (n.strip(), sp[0].strip()))
-orig = open(originalLabels["path"], "rt")
+orig = open(originalLabels, "rt")
print(orig.read())
diff --git a/workflows/pangenome-generate/minimap2.cwl b/workflows/pangenome-generate/minimap2.cwl
index bf19ef7..42d1dce 100644
--- a/workflows/pangenome-generate/minimap2.cwl
+++ b/workflows/pangenome-generate/minimap2.cwl
@@ -12,7 +12,7 @@ hints:
ResourceRequirement:
coresMin: 8
coresMax: 32
- ramMin: $(7 * 1024)
+ ramMin: $(9 * 1024)
outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
stdout: $(inputs.readsFA.nameroot).paf
baseCommand: minimap2
diff --git a/workflows/pangenome-generate/relabel-seqs.cwl b/workflows/pangenome-generate/relabel-seqs.cwl
index 2b780d4..c1f17a4 100644
--- a/workflows/pangenome-generate/relabel-seqs.cwl
+++ b/workflows/pangenome-generate/relabel-seqs.cwl
@@ -3,6 +3,10 @@ class: CommandLineTool
inputs:
readsFA: File[]
subjects: string[]
+ script:
+ type: File
+ default: {class: File, location: relabel-seqs.py}
+ inputBinding: {}
outputs:
relabeledSeqs:
type: File
@@ -15,11 +19,32 @@ outputs:
requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
- listing:
- - entry: {$include: relabel-seqs.py}
- entryname: relabel-seqs.py
+ listing: |
+ ${
+ var i = 0;
+ var b = 1;
+ var out = [];
+ for (; i < inputs.readsFA.length; i++) {
+ var block = [];
+ var sub = [];
+ for (; i < (b*150) && i < inputs.readsFA.length; i++) {
+ block.push(inputs.readsFA[i]);
+ sub.push(inputs.subjects[i]);
+ }
+ out.push({
+ entryname: "block"+b,
+ entry: JSON.stringify(block)
+ });
+ out.push({
+ entryname: "subs"+b,
+ entry: JSON.stringify(sub)
+ });
+ b++;
+ }
+ return out;
+ }
hints:
DockerRequirement:
dockerPull: commonworkflowlanguage/cwltool_module
stdout:
-baseCommand: [python, relabel-seqs.py]
+baseCommand: [python]
diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py
index 1188ceb..6b022a0 100644
--- a/workflows/pangenome-generate/relabel-seqs.py
+++ b/workflows/pangenome-generate/relabel-seqs.py
@@ -1,5 +1,17 @@
-reads = $(inputs.readsFA)
-subjects = $(inputs.subjects)
+import os
+import json
+
+def readitems(stem):
+ items = []
+ b = 1
+ while os.path.exists("%s%i" % (stem, b)):
+ with open("%s%i" % (stem, b)) as f:
+ items.extend(json.load(f))
+ b += 1
+ return items
+
+reads = readitems("block")
+subjects = readitems("subs")
relabeled_fasta = open("relabeledSeqs.fasta", "wt")
original_labels = open("originalLabels.ttl", "wt")
@@ -7,12 +19,12 @@ original_labels = open("originalLabels.ttl", "wt")
for i, r in enumerate(reads):
with open(r["path"], "rt") as fa:
label = fa.readline()
- original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \\"%s\\" .\\n" % (subjects[i], label[1:].strip().replace('"', '\\\\"')))
- relabeled_fasta.write(">"+subjects[i]+"\\n")
+ original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subjects[i], label[1:].strip().replace('"', '\\"')))
+ relabeled_fasta.write(">"+subjects[i]+"\n")
data = fa.read(8096)
while data:
relabeled_fasta.write(data)
- endswithnewline = data.endswith("\\n")
+ endswithnewline = data.endswith("\n")
data = fa.read(8096)
if not endswithnewline:
- relabeled_fasta.write("\\n")
+ relabeled_fasta.write("\n")
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-26 20:27:35 +0000