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authorPeter Amstutz2020-11-09 17:32:05 -0500
committerGitHub2020-11-09 17:32:05 -0500
commit74d46196ae69c0c557f64593910ada48d84b3654 (patch)
tree57c7df946e1aa1f2054eb49379439ebee4d4c0e6 /workflows
parentb311e2ec0f1d02cf16152855dd8bdd760ed4578b (diff)
parent98a80bd64d8a495b8fddffdef6e07e5a3fbea1e3 (diff)
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Merge pull request #105 from arvados/fasta-subset-from-query
Extract subset of the all-sequences fasta by running a sparql query. Also includes some tweaks to the permalinks.
Diffstat (limited to 'workflows')
-rw-r--r--workflows/pangenome-generate/arv-main.cwl2
-rw-r--r--workflows/pangenome-generate/collect-seqs.cwl2
-rw-r--r--workflows/pangenome-generate/collect-seqs.py2
-rw-r--r--workflows/pangenome-generate/from_sparql.cwl23
-rw-r--r--workflows/pangenome-generate/from_sparql.py8
-rwxr-xr-xworkflows/update-workflows.sh2
6 files changed, 35 insertions, 4 deletions
diff --git a/workflows/pangenome-generate/arv-main.cwl b/workflows/pangenome-generate/arv-main.cwl
index dae47e6..1d71ee3 100644
--- a/workflows/pangenome-generate/arv-main.cwl
+++ b/workflows/pangenome-generate/arv-main.cwl
@@ -36,7 +36,7 @@ steps:
run: collect-seqs.cwl
in:
src_project: src_project
- schema: metadataSchema
+ metadataSchema: metadataSchema
exclude: exclude
out: [relabeledSeqs, mergedMetadata]
pangenome-generate:
diff --git a/workflows/pangenome-generate/collect-seqs.cwl b/workflows/pangenome-generate/collect-seqs.cwl
index 3511df1..635108f 100644
--- a/workflows/pangenome-generate/collect-seqs.cwl
+++ b/workflows/pangenome-generate/collect-seqs.cwl
@@ -25,7 +25,7 @@ inputs:
src_project:
type: string
inputBinding: {position: 2}
- schema:
+ metadataSchema:
type: File
inputBinding: {position: 3}
exclude:
diff --git a/workflows/pangenome-generate/collect-seqs.py b/workflows/pangenome-generate/collect-seqs.py
index af4a0dc..1a0807c 100644
--- a/workflows/pangenome-generate/collect-seqs.py
+++ b/workflows/pangenome-generate/collect-seqs.py
@@ -38,7 +38,7 @@ for item in validated:
pdh = item["portable_data_hash"]
with arvados.collection.CollectionReader(pdh, api_client=api, keep_client=keepclient) as col:
with col.open("sequence.fasta", "rt") as fa:
- subject = "http://collections.lugli.arvadosapi.com/c=%s/sequence.fasta" % pdh
+ subject = "http://covid19.genenetwork.org/resource/%s" % pdh
label = fa.readline().strip()
merged_metadata.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subject, label[1:].replace('"', '\\"')))
skip = (subject in blacklist or label[1:] in blacklist)
diff --git a/workflows/pangenome-generate/from_sparql.cwl b/workflows/pangenome-generate/from_sparql.cwl
new file mode 100644
index 0000000..5bc0792
--- /dev/null
+++ b/workflows/pangenome-generate/from_sparql.cwl
@@ -0,0 +1,23 @@
+cwlVersion: v1.1
+class: CommandLineTool
+requirements:
+ DockerRequirement:
+ dockerFile: |
+ FROM debian:10
+ RUN apt-get update && apt-get -yq --no-install-recommends install samtools python3-rdflib
+ dockerImageId: rdflib-and-samtools
+inputs:
+ script:
+ type: File
+ default:
+ class: File
+ location: from_sparql.py
+ metadata: File
+ fasta:
+ type: File
+ secondaryFiles: [.fai]
+ query: string
+stdout: selected.fasta
+outputs:
+ selected: stdout
+arguments: [python3, $(inputs.script), $(inputs.metadata), $(inputs.fasta), $(inputs.query)]
diff --git a/workflows/pangenome-generate/from_sparql.py b/workflows/pangenome-generate/from_sparql.py
new file mode 100644
index 0000000..4610cad
--- /dev/null
+++ b/workflows/pangenome-generate/from_sparql.py
@@ -0,0 +1,8 @@
+from rdflib import Graph
+import sys
+import subprocess
+g = Graph()
+g.parse(sys.argv[1], format="nt")
+res = g.query(sys.argv[3])
+for r in res:
+ subprocess.run(["samtools", "faidx", sys.argv[2], r[0]])
diff --git a/workflows/update-workflows.sh b/workflows/update-workflows.sh
index 3b69a58..5182ec4 100755
--- a/workflows/update-workflows.sh
+++ b/workflows/update-workflows.sh
@@ -1,3 +1,3 @@
#!/bin/sh
arvados-cwl-runner --project-uuid=lugli-j7d0g-5hswinmpyho8dju --update-workflow=lugli-7fd4e-2zp9q4jo5xpif9y fastq2fasta/fastq2fasta.cwl
-arvados-cwl-runner --project-uuid=lugli-j7d0g-5hswinmpyho8dju --update-workflow=lugli-7fd4e-mqfu9y3ofnpnho1 pangenome-generate/arv-main.cwl
+arvados-cwl-runner --project-uuid=lugli-j7d0g-5hswinmpyho8dju --update-workflow=lugli-7fd4e-mqfu9y3ofnpnho1 pangenome-generate/collect-seqs.cwl