diff --git a/hippunfold/workflow/rules/downloads.smk b/hippunfold/workflow/rules/downloads.smk index 32f6e564..04ae6037 100644 --- a/hippunfold/workflow/rules/downloads.smk +++ b/hippunfold/workflow/rules/downloads.smk @@ -1,8 +1,10 @@ # create rules for downloading each atlas, since output files need to be specified # without using wildcards -for atlas in config['atlas']: - rule: - name: f"download_atlas_{atlas}" +for atlas in config["atlas"]: + + rule: + name: + f"download_atlas_{atlas}" params: url=config["atlas_links_url"][atlas], output: @@ -13,13 +15,17 @@ for atlas in config['atlas']: "wget https://{params.url} -O {output.model_zip}" rule: - name: f"unzip_download_atlas_{atlas}" + name: + f"unzip_download_atlas_{atlas}" input: model_zip=os.path.join(download_dir, atlas + ".zip"), params: dir=os.path.join(download_dir, atlas), output: - [expand(Path(download_dir)/path,hemi=config['hemi']) for key,path in config['atlas_files'][atlas].items()] + [ + expand(Path(download_dir) / path, hemi=config["hemi"]) + for key, path in config["atlas_files"][atlas].items() + ], shell: "unzip {input.model_zip} -d {params.dir}" diff --git a/hippunfold/workflow/rules/qc.smk b/hippunfold/workflow/rules/qc.smk index 1989b5a7..43459a3f 100644 --- a/hippunfold/workflow/rules/qc.smk +++ b/hippunfold/workflow/rules/qc.smk @@ -50,7 +50,8 @@ rule get_subfield_vols_subj: hemi=config["hemi"], allow_missing=True, ), - lookup_tsv=lambda wildcards: Path(download_dir) / config["atlas_files"][wildcards.atlas]["subfields_list"] + lookup_tsv=lambda wildcards: Path(download_dir) + / config["atlas_files"][wildcards.atlas]["subfields_list"], group: "subj" output: