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-rw-r--r--bh20seqanalyzer/main.py9
1 files changed, 6 insertions, 3 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 9164190..9a36cae 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -30,6 +30,7 @@ def validate_upload(api, collection, validated_project,
try:
metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"]
+ sample_id = metadata_content["sample"]["sample_id"]
add_lc_filename(metadata_content, metadata_content["id"])
valid = qc_metadata(metadata_content) and valid
except Exception as e:
@@ -51,7 +52,7 @@ def validate_upload(api, collection, validated_project,
logging.info("Expected %s but magic says it should be %s", n, tgt)
valid = False
elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
- start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n)
+ start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n, sample_id)
return False
if tgt is None:
valid = False
@@ -108,7 +109,8 @@ def run_workflow(api, parent_project, workflow_uuid, name, inputobj):
def start_fastq_to_fasta(api, collection,
analysis_project,
fastq_workflow_uuid,
- tgt):
+ tgt,
+ sample_id):
params = {
"metadata": {
@@ -118,7 +120,8 @@ def start_fastq_to_fasta(api, collection,
"ref_fasta": {
"class": "File",
"location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta"
- }
+ },
+ "sample_id": sample_id
}
if tgt.startswith("reads.fastq"):