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Klaus 232 rclone conf visibility #78

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Merged
SkepticRaven merged 2 commits into from
Sep 5, 2025
Merged

Klaus 232 rclone conf visibility #78

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4399fd8
Adding rclone config as input to processes
SkepticRaven Sep 3, 2025
75fed47
Merge branch 'main' into KLAUS-232-rclone-conf-visibility
SkepticRaven Sep 4, 2025
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1 change: 1 addition & 0 deletions nextflow/configs/profiles/sumner2.config
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,7 @@ params {
globus_remote_endpoint = "70850914-722d-11e7-aa01-22000bf2d287" // JAX T2 storage endpoint
globus_remote_folder = "/tier2/vkumar/"
dropbox_prefix = "labdropbox:\"/KumarLab's shared workspace/VideoData/MDS_Tests/\""
rclone_config = "/projects/kumar-lab/meta/secrets/tokens/rclone_dropbox.conf"
}

apptainer {
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9 changes: 6 additions & 3 deletions nextflow/modules/remote_io.nf
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Expand Up @@ -51,6 +51,7 @@ process FILTER_UNPROCESSED_DROPBOX {
input:
path test_files
val dropbox_prefix
path rclone_config

output:
path "unprocessed_files.txt", emit: unprocessed_files
Expand All @@ -62,7 +63,7 @@ process FILTER_UNPROCESSED_DROPBOX {
touch unprocessed_files.txt
while read test_file; do
test_pose=\${test_file/.*}_pose_est_v6.h5
rclone ls ${dropbox_prefix}\${test_pose} > /dev/null 2>&1
rclone ls --config=${rclone_config} ${dropbox_prefix}\${test_pose} > /dev/null 2>&1
if [[ \$? != 0 ]]; then
echo \$test_file >> unprocessed_files.txt
fi
Expand Down Expand Up @@ -122,14 +123,15 @@ process GET_DATA_FROM_DROPBOX {
input:
path files_to_transfer
val dropbox_prefix
path rclone_config

output:
path "fetched_files.txt", emit: remote_files

script:
"""
echo ${dropbox_prefix}
rclone copy --transfers=1 --include-from ${files_to_transfer} ${dropbox_prefix} retrieved_files/.
rclone copy --config=${rclone_config} --transfers=1 --include-from ${files_to_transfer} ${dropbox_prefix} retrieved_files/.
find \$(pwd)/retrieved_files/ -type f > fetched_files.txt
"""
}
Expand All @@ -142,9 +144,10 @@ process PUT_DATA_TO_DROPBOX {
path file_to_upload
tuple path(result_file), val(publish_filename)
val dropbox_prefix
path rclone_config

script:
"""
rclone copy --transfers=1 ${result_file} ${dropbox_prefix}/${publish_filename}
rclone copy --config=${rclone_config} --transfers=1 ${result_file} ${dropbox_prefix}/${publish_filename}
"""
}
4 changes: 2 additions & 2 deletions nextflow/workflows/io.nf
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Expand Up @@ -24,8 +24,8 @@ workflow PREPARE_DATA {
if (location == "local") {
file_batch = FILTER_LOCAL_BATCH(all_valid_files, params.ignore_invalid_inputs, params.filter_processed, params.pubdir).process_filelist
} else if (location == "dropbox") {
in_video_list = FILTER_UNPROCESSED_DROPBOX(all_valid_files, params.dropbox_prefix).unprocessed_files
file_batch = GET_DATA_FROM_DROPBOX(in_video_list, params.dropbox_prefix).remote_files
in_video_list = FILTER_UNPROCESSED_DROPBOX(all_valid_files, params.dropbox_prefix, params.rclone_config).unprocessed_files
file_batch = GET_DATA_FROM_DROPBOX(in_video_list, params.dropbox_prefix, params.rclone_config).remote_files
} else if (location == "globus") {
CHECK_GLOBUS_AUTH()
in_video_list = FILTER_UNPROCESSED_GLOBUS(params.globus_remote_endpoint, all_valid_files).unprocessed_files
Expand Down