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Fix command calls in jabs_classifiers nextflow module #90

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Merged
bergsalex merged 1 commit into from
Oct 3, 2025
Merged

Fix command calls in jabs_classifiers nextflow module #90

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19 changes: 15 additions & 4 deletions nextflow/modules/jabs_classifiers.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -106,7 +106,12 @@ process GENERATE_BEHAVIOR_TABLES {
script:
"""
behavior_command="--behavior ${classifiers.collect { entry -> "$entry.key --stitch_gap $entry.value.stitch_value --min_bout_length $entry.value.filter_value" }.join(' --behavior ')}"
python3 /JABS-postprocess/generate_behavior_tables.py --project_folder . --feature_folder . --out_prefix ${in_pose.baseName} --out_bin_size 5 \${behavior_command}
jabs-postprocess generate-tables \
--project_folder . \
--feature_folder . \
--out_prefix ${in_pose.baseName} \
--out_bin_size 5 \
\${behavior_command}
"""
}

Expand Down Expand Up @@ -139,7 +144,12 @@ process PREDICT_HEURISTICS {
"""
for classifier in ${heuristic_classifiers.join(' ')};
do
python3 /JABS-postprocess/heuristic_classify.py --project_folder . --feature_folder . --behavior_config \${classifier} --out_prefix ${in_pose.baseName} --out_bin_size 5
jabs-postprocess heuristic-classify \
--project-folder . \
--feature-folder . \
--behavior-config \${classifier} \
--out-prefix ${in_pose.baseName} \
--out_bin_size 5
done
"""
}
Expand Down Expand Up @@ -211,7 +221,7 @@ process AGGREGATE_BOUT_TABLES {
echo "Input tables found:" >> merge_log.txt
ls table_staging/*.csv >> merge_log.txt

uv run python -m jabs_postprocess.cli.main merge-multiple-tables \\
jabs-postprocess merge-multiple-tables \\
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--table-folder table_staging \\
--table-pattern "*_bouts.csv" \\
--output-prefix merged \\
Expand All @@ -222,4 +232,5 @@ process AGGREGATE_BOUT_TABLES {
echo "Merge completed. Output files:" >> merge_log.txt
ls merged_*_bouts_merged.csv >> merge_log.txt 2>/dev/null || echo "No merged files generated" >> merge_log.txt
"""
}
}