From d5b6b8514e99d818aaca35fcf6ab77c593a02503 Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Thu, 19 Dec 2024 16:51:46 -0500 Subject: [PATCH 1/2] update session column --- helper_scripts/symlink_neurobagel_results_on_bic.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/helper_scripts/symlink_neurobagel_results_on_bic.sh b/helper_scripts/symlink_neurobagel_results_on_bic.sh index 201ef2c..0d1a52e 100644 --- a/helper_scripts/symlink_neurobagel_results_on_bic.sh +++ b/helper_scripts/symlink_neurobagel_results_on_bic.sh @@ -7,8 +7,8 @@ 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) From 4799de1151604b060360db27860dd98e0ce8d26e Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Thu, 19 Dec 2024 16:53:04 -0500 Subject: [PATCH 2/2] update docstring --- helper_scripts/symlink_neurobagel_results_on_bic.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/helper_scripts/symlink_neurobagel_results_on_bic.sh b/helper_scripts/symlink_neurobagel_results_on_bic.sh index 0d1a52e..8ddc841 100644 --- a/helper_scripts/symlink_neurobagel_results_on_bic.sh +++ b/helper_scripts/symlink_neurobagel_results_on_bic.sh @@ -2,7 +2,7 @@ # USAGE: ./symlink_neurobagel_results_on_bic.sh -# 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