From 366e110f75f774a0f7ed106382833513a8a63e93 Mon Sep 17 00:00:00 2001 From: Alex Stuckey Date: Mon, 9 Sep 2024 13:49:34 +1200 Subject: [PATCH] try more debugging --- query_metamist.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/query_metamist.py b/query_metamist.py index 35a04bc..f2fd97f 100644 --- a/query_metamist.py +++ b/query_metamist.py @@ -1,8 +1,8 @@ from argparse import ArgumentParser from typing import Any -from cpg_utils.config import get_config -from cpg_utils.hail_batch import Batch, command, get_batch, image_path, output_path +from cpg_utils.config import get_config, image_path, output_path +from cpg_utils.hail_batch import Batch, command, get_batch from graphql import DocumentNode from hailtop.batch.job import BashJob @@ -36,7 +36,7 @@ def get_assays(project: str, sgids: list[str]) -> dict[str, list[str]]: Returns: dict: A dictionary where each key is a sequencing group ID and each value is a list of read locations for that sequencing group. """ - sg_assay_map = {} + sg_assay_map: dict[str, list[str]] = {} # Use the query template above to query the sequencing groups and assays query_response: dict[str, Any] = query( @@ -93,8 +93,6 @@ def main(project: str, sgids: list[str], last_name: str): for sg, files in file_dict.items(): assert len(files) == 2 - print(f"{sg}: {files}") - j: BashJob = b.new_job(name="FastQE", attributes={"tool": "fastqe"}) j.image(image_path("fastqe")) j.storage("2Gi")