def __init__(self, scratch_dir, workspace_url, callback_url, srv_wiz_url,
provenance):
self.scratch_dir = scratch_dir
self.workspace_url = workspace_url
self.callback_url = callback_url
self.srv_wiz_url = srv_wiz_url
self.provenance = provenance
# from the provenance, extract out the version to run by exact hash if possible
self.my_version = 'release'
if len(provenance) > 0:
if 'subactions' in provenance[0]:
self.my_version = self.get_version_from_subactions(
'kb_Bwa', provenance[0]['subactions'])
print('Running kb_Bwa version = ' + self.my_version)
self.ws = Workspace(self.workspace_url)
self.bwa = BwaRunner(self.scratch_dir)
self.parallel_runner = KBParallel(self.callback_url)
self.qualimap = kb_QualiMap(self.callback_url)
def run_batch(self, reads_refs, params):
"""
Runs HISAT2 in batch mode.
reads_refs should be a list of dicts, where each looks like the following:
{
"ref": reads object reference,
"condition": condition for that ref (string)
}
"""
# build task list and send it to KBParallel
tasks = list()
set_name = get_object_names(
[params["sampleset_ref"]],
self.workspace_url)[params["sampleset_ref"]]
for idx, reads_ref in enumerate(reads_refs):
single_param = dict(params) # need a copy of the params
single_param["build_report"] = 0
single_param["sampleset_ref"] = reads_ref["ref"]
if "condition" in reads_ref:
single_param["condition"] = reads_ref["condition"]
else:
single_param["condition"] = "unspecified"
tasks.append({
"module_name": "kb_hisat2",
"function_name": "run_hisat2",
"version": self.my_version,
"parameters": single_param
})
# UNCOMMENT BELOW FOR LOCAL TESTING
batch_run_params = {
"tasks": tasks,
"runner": "parallel",
# "concurrent_local_tasks": 3,
# "concurrent_njsw_tasks": 0,
"max_retries": 2
}
parallel_runner = KBParallel(self.callback_url)
results = parallel_runner.run_batch(batch_run_params)["results"]
alignment_items = list()
alignments = dict()
for idx, result in enumerate(results):
# idx of the result is the same as the idx of the inputs AND reads_refs
if result["is_error"] != 0:
raise RuntimeError(
"Failed a parallel run of HISAT2! {}".format(
result["result_package"]["error"]))
reads_ref = tasks[idx]["parameters"]["sampleset_ref"]
alignment_items.append({
"ref":
result["result_package"]["result"][0]["alignment_objs"]
[reads_ref]["ref"],
"label":
reads_refs[idx].get("condition",
params.get("condition", "unspecified"))
})
alignments[reads_ref] = result["result_package"]["result"][0][
"alignment_objs"][reads_ref]
# build the final alignment set
output_ref = self.upload_alignment_set(
alignment_items, set_name + params["alignmentset_suffix"],
params["ws_name"])
return (alignments, output_ref)