diff --git a/src/nbis/snakemake.py b/src/nbis/snakemake.py index 1633ee5..59503e3 100644 --- a/src/nbis/snakemake.py +++ b/src/nbis/snakemake.py @@ -184,6 +184,17 @@ def directory_option(): ) +def report_option() -> Callable[[FC], FC]: + """Add snakemake report option""" + func = click.option( + "--report", + help=("generate snakemake report"), + is_flag=True, + default=False, + ) + return func + + def format_snakemake_help(smkfile, *, default=None): """Return docstring from snakemake file. diff --git a/src/nbis/wrappers.py b/src/nbis/wrappers.py index 34c09fb..1e3c613 100644 --- a/src/nbis/wrappers.py +++ b/src/nbis/wrappers.py @@ -21,8 +21,10 @@ def run(self, *args, **kwargs): raise NotImplementedError -def snakemake(targets=None, options=None, snakefile=None): +def snakemake(*, targets=None, options=None, snakefile=None): """Run snakemake workflows.""" + if isinstance(options, list): + options = " ".join(options) cmdlist = [ "snakemake", f"{'-s ' + str(snakefile) if snakefile else ''}",