diff options
Diffstat (limited to 'bh20seqanalyzer/main.py')
| -rw-r--r-- | bh20seqanalyzer/main.py | 48 |
1 files changed, 34 insertions, 14 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 31ad4c4..794ce27 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -40,20 +40,21 @@ def validate_upload(api, collection, validated_project, if valid: tgt = None - for n in ("sequence.fasta", "reads.fastq"): + paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"} + for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): if n not in col: continue - with col.open(n) as qf: - tgt = qc_fasta(qf) - if tgt != n: + with col.open(n, 'rb') as qf: + tgt = qc_fasta(qf)[0] + if tgt != n and tgt != paired.get(n): logging.info("Expected %s but magic says it should be %s", n, tgt) valid = False - elif tgt == "reads.fastq": - start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid) + 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) return False if tgt is None: valid = False - logging.warn("Upload '%s' does not contain sequence.fasta or reads.fastq", collection["name"]) + logging.warn("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"]) dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], ["portable_data_hash", "=", col.portable_data_hash()]]).execute() @@ -95,6 +96,7 @@ def run_workflow(api, parent_project, workflow_uuid, name, inputobj): tmp.name] logging.info("Running %s" % ' '.join(cmd)) comp = subprocess.run(cmd, capture_output=True) + logging.info("Submitted %s", comp.stdout) if comp.returncode != 0: logging.error(comp.stderr.decode('utf-8')) @@ -103,12 +105,10 @@ def run_workflow(api, parent_project, workflow_uuid, name, inputobj): def start_fastq_to_fasta(api, collection, analysis_project, - fastq_workflow_uuid): - newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", { - "fastq_forward": { - "class": "File", - "location": "keep:%s/reads.fastq" % collection["portable_data_hash"] - }, + fastq_workflow_uuid, + tgt): + + params = { "metadata": { "class": "File", "location": "keep:%s/metadata.yaml" % collection["portable_data_hash"] @@ -117,7 +117,24 @@ def start_fastq_to_fasta(api, collection, "class": "File", "location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta" } - }) + } + + if tgt.startswith("reads.fastq"): + params["fastq_forward"] = { + "class": "File", + "location": "keep:%s/%s" % (collection["portable_data_hash"], tgt) + } + elif tgt.startswith("reads_1.fastq"): + params["fastq_forward"] = { + "class": "File", + "location": "keep:%s/reads_1.%s" % (collection["portable_data_hash"], tgt[8:]) + } + params["fastq_reverse"] = { + "class": "File", + "location": "keep:%s/reads_2.%s" % (collection["portable_data_hash"], tgt[8:]) + } + + newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", params) api.collections().update(uuid=collection["uuid"], body={"owner_uuid": newproject["uuid"]}).execute() @@ -222,6 +239,7 @@ def main(): parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') parser.add_argument('--kickoff', action="store_true") + parser.add_argument('--once', action="store_true") args = parser.parse_args() api = arvados.api() @@ -265,4 +283,6 @@ def main(): args.pangenome_analysis_project, args.latest_result_collection) + if args.once: + break time.sleep(15) |