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Remove unnecessary arguments from cubids apply #317

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Jun 4, 2024
Merged

Remove unnecessary arguments from cubids apply #317

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12 changes: 3 additions & 9 deletions cubids/workflows.py
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Original file line number Diff line number Diff line change
Expand Up @@ -359,10 +359,8 @@ def apply(
acq_group_level,
config,
edited_summary_tsv,
edited_tsv_prefix,
files_tsv,
new_tsv_prefix,
output_prefix,
container,
):
"""Apply the tsv changes.
Expand All @@ -379,14 +377,10 @@ def apply(
Path to the grouping config file.
edited_summary_tsv : :obj:`pathlib.Path`
Path to the edited summary tsv.
edited_tsv_prefix : :obj:`pathlib.Path`
Path to the edited tsv prefix.
files_tsv : :obj:`pathlib.Path`
Path to the files tsv.
new_tsv_prefix : :obj:`pathlib.Path`
Path to the new tsv prefix.
output_prefix : :obj:`pathlib.Path`
Output filename prefix.
container : :obj:`str`
Container in which to run the workflow.
"""
Expand All @@ -412,8 +406,8 @@ def apply(
# Run it through a container
container_type = _get_container_type(container)
bids_dir_link = str(bids_dir.absolute()) + ":/bids"
input_summary_tsv_dir_link = str(edited_tsv_prefix.parent.absolute()) + ":/in_summary_tsv:ro"
input_files_tsv_dir_link = str(edited_tsv_prefix.parent.absolute()) + ":/in_files_tsv:ro"
input_summary_tsv_dir_link = str(edited_summary_tsv.parent.absolute()) + ":/in_summary_tsv:ro"
input_files_tsv_dir_link = str(edited_summary_tsv.parent.absolute()) + ":/in_files_tsv:ro"
output_tsv_dir_link = str(new_tsv_prefix.parent.absolute()) + ":/out_tsv:rw"

# FROM BOND-GROUP
Expand All @@ -422,7 +416,7 @@ def apply(
input_config_dir_link = str(config.parent.absolute()) + ":/in_config:ro"
linked_input_config = "/in_config/" + config.name

linked_output_prefix = "/tsv/" + output_prefix.name
linked_output_prefix = "/tsv/" + new_tsv_prefix.name

####
linked_input_summary_tsv = "/in_summary_tsv/" + edited_summary_tsv.name
Expand Down