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[MNT] Update session column in BIC symlink script #3

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merged 2 commits into from
Dec 19, 2024
Merged

[MNT] Update session column in BIC symlink script #3

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d5b6b85
update session column
alyssadai Dec 19, 2024
4799de1
update docstring
alyssadai Dec 19, 2024
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6 changes: 3 additions & 3 deletions helper_scripts/symlink_neurobagel_results_on_bic.sh
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Expand Up @@ -2,13 +2,13 @@

# USAGE: ./symlink_neurobagel_results_on_bic.sh <PATH TO NEUROBAGEL QUERY RESULTS TSV> <DESTINATION DIRECTORY FOR SYMLINKS>

# USAGE EXAMPLE: ./symlink_neurobagel_results_on_bic.sh cohort-participant-machine-results.tsv /home/new_neurobagel_cohort
# USAGE EXAMPLE: ./symlink_neurobagel_results_on_bic.sh neurobagel-query-results.tsv /home/new_neurobagel_cohort

RESULTS_TSV=$1
TARGET_DIR=$2

SESSION_PATH_COL="SessionFilePath"
SESSION_PATH_COL_IDX=5
SESSION_PATH_COL="ImagingSessionPath"
SESSION_PATH_COL_IDX=6

# Extract session path column and remove i) the column header, ii) any empty lines, iii) any "protected" lines, and iv) duplicates (just in case)
session_paths=$(cut -d $'\t' -f $SESSION_PATH_COL_IDX $RESULTS_TSV | grep -v "${SESSION_PATH_COL}" | grep -v "^$" | grep -v "protected" | sort | uniq)
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