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Add runmode (full, fast) for debugging purposes (#26)
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@alejoe91
alejoe91 authored Nov 4, 2024
1 parent fbdeb95 commit dc7cbbe
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5 changes: 3 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -145,8 +145,9 @@ In Nextflow, the The `-resume` argument enables the caching mechanism.
The following global parameters can be passed to the pipeline:

```bash
--n_jobs N_JOBS (for local deployment, how many jobs to run in parallel)
--sorter {kilosort25,kilosort4,spykingcircus2}
--n_jobs N_JOBS For local deployment, how many jobs to run in parallel
--sorter {kilosort25,kilosort4,spykingcircus2} Which sorter to use
--runmode {full,fast} The runmode to use. Default is 'fThe 'fast' mode skips some steps (e.g., motion correction) to speed up the processing. Default is 'full'
```
## Process-specific parameters
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90 changes: 68 additions & 22 deletions pipeline/main_local.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -28,23 +28,69 @@ else
}
println "Using SORTER: ${sorter}"

// set runmode
if ("runmode" in params_keys) {
runmode = params.runmode
}
else
{
runmode = "full"
}
println "Using RUNMODE: ${runmode}"

if (!params_keys.contains('job_dispatch_args')) {
params.job_dispatch_args = ""
job_dispatch_args = ""
}
else {
job_dispatch_args = params.job_dispatch_args
}
if (!params_keys.contains('preprocessing_args')) {
params.preprocessing_args = ""
preprocessing_args = ""
}
else {
preprocessing_args = params.preprocessing_args
}
if (!params_keys.contains('spikesorting_args')) {
params.spikesorting_args = ""
spikesorting_args = ""
}
else {
spikesorting_args = params.spikesorting_args
}
if (!params_keys.contains('postprocessing_args')) {
params.postprocessing_args = ""
postprocessing_args = ""
}
else {
postprocessing_args = params.postprocessing_args
}
if (!params_keys.contains('unit_classifier_args')) {
unit_classifier_args = ""
}
else {
unit_classifier_args = params.unit_classifier_args
}
if (!params_keys.contains('nwb_subject_args')) {
params.nwb_subject_args = ""
nwb_subject_args = ""
}
else {
nwb_subject_args = params.nwb_subject_args
}
if (!params_keys.contains('nwb_ecephys_args')) {
params.nwb_ecephys_args = ""
nwb_ecephys_args = ""
}
else {
nwb_ecephys_args = params.nwb_ecephys_args
}

if (runmode == 'fast'){
preprocessing_args = "--motion skip"
postprocessing_args = "--skip-extensions spike_locations,principal_components"
unit_classifier_args = "--skip-metrics-recomputation"
nwb_ecephys_args = "--skip-lfp"
println "Running in fast mode. Setting parameters:"
println "preprocessing_args: ${preprocessing_args}"
println "postprocessing_args: ${postprocessing_args}"
println "unit_classifier_args: ${unit_classifier_args}"
println "nwb_ecephys_args: ${nwb_ecephys_args}"
}


Expand Down Expand Up @@ -145,7 +191,7 @@ process job_dispatch {
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.job_dispatch_args}
./run ${job_dispatch_args}
max_duration_min=\$(python get_max_recording_duration_min.py)
echo "MAX DURATION: \$max_duration_min"
Expand Down Expand Up @@ -193,7 +239,7 @@ process preprocessing {
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.preprocessing_args} --n-jobs ${n_jobs}
./run ${preprocessing_args} --n-jobs ${n_jobs}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -229,14 +275,14 @@ process spikesort_kilosort25 {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-spikesort-kilosort25.git" capsule-repo
git -C capsule-repo checkout c7b2d11ea0c258a0d07c28c105d365553ccfaf43 --quiet
git -C capsule-repo checkout 8c8987260a27c75b1f523d306b40a16962a97ea6 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.spikesorting_args} --n-jobs ${n_jobs}
./run ${spikesorting_args} --n-jobs ${n_jobs}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -272,14 +318,14 @@ process spikesort_kilosort4 {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-spikesort-kilosort4.git" capsule-repo
git -C capsule-repo checkout 2183dc930959c4e8007f7a8fbcc04f0fc72648ab --quiet
git -C capsule-repo checkout 6b4e6cd5bf90e05be7ce7e2de9a28f4dcfa02c29 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.spikesorting_args} --n-jobs ${n_jobs}
./run ${spikesorting_args} --n-jobs ${n_jobs}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -315,14 +361,14 @@ process spikesort_spykingcircus2 {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-spikesort-spykingcircus2.git" capsule-repo
git -C capsule-repo checkout 6f4ea112127d1727ba81040cf1563bcf9a40ca7d --quiet
git -C capsule-repo checkout 1f88d6741e33bf9a0e6e23107c64f3c7ad17b5e4 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.spikesorting_args} --n-jobs ${n_jobs}
./run ${spikesorting_args} --n-jobs ${n_jobs}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -360,14 +406,14 @@ process postprocessing {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-postprocessing.git" capsule-repo
git -C capsule-repo checkout f63b9b16c5ababd75826445f1f71a44298feeff2 --quiet
git -C capsule-repo checkout 1bcc57e0b6be45dc39afd3ef18e0ad678173cc2e --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.postprocessing_args} --n-jobs ${n_jobs}
./run ${postprocessing_args} --n-jobs ${n_jobs}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -434,14 +480,14 @@ process unit_classifier {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-unit-classifier.git" capsule-repo
git -C capsule-repo checkout 0231bdaa9cb1a812e55b0c938167049ba0ea62fe --quiet
git -C capsule-repo checkout a5f1e947c7099090cca2c8250b9bad0b796a67dd --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run
./run ${unit_classifier_args}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -477,7 +523,7 @@ process visualization {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-visualization.git" capsule-repo
git -C capsule-repo checkout bc4a6b7ed63624f7f1b280c0e23cf82cf330ae6a --quiet
git -C capsule-repo checkout f58ab7cda7757b4703da049a160a5677c2cd9c54 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -524,7 +570,7 @@ process results_collector {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-results-collector.git" capsule-repo
git -C capsule-repo checkout dea3ac29ac8e82322b2a4488b56b6720861cc80a --quiet
git -C capsule-repo checkout 73cb90e9c321a6c06012681ca08d93b71e99d952 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -567,7 +613,7 @@ process nwb_subject {
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.nwb_subject_args}
./run ${nwb_subject_args}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -605,7 +651,7 @@ process nwb_ecephys {
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run ${params.nwb_ecephys_args}
./run ${nwb_ecephys_args}
echo "[${task.tag}] completed!"
"""
Expand Down
41 changes: 33 additions & 8 deletions pipeline/main_slurm.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,16 @@ else
}
println "Using SORTER: ${sorter}"

// set runmode
if ("runmode" in params_keys) {
runmode = params.runmode
}
else
{
runmode = "full"
}
println "Using RUNMODE: ${runmode}"

if (!params_keys.contains('job_dispatch_args')) {
params.job_dispatch_args = ""
}
Expand All @@ -31,13 +41,28 @@ if (!params_keys.contains('spikesorting_args')) {
if (!params_keys.contains('postprocessing_args')) {
params.postprocessing_args = ""
}
if (!params_keys.contains('unit_classifier_args')) {
params.unit_classifier_args = ""
}
if (!params_keys.contains('nwb_subject_args')) {
params.nwb_subject_args = ""
}
if (!params_keys.contains('nwb_ecephys_args')) {
params.nwb_ecephys_args = ""
}

if (runmode == 'fast'){
params.preprocessing_args = "--motion skip"
params.postprocessing_args = "--skip-extensions spike_locations,principal_components"
params.unit_classifier_args = "--skip-metrics-recomputation"
params.nwb_ecephys_args = "--skip-lfp"
println "Running in fast mode. Setting parameters:"
println "preprocessing_args: ${params.preprocessing_args}"
println "postprocessing_args: ${params.postprocessing_args}"
println "unit_classifier_args: ${params.unit_classifier_args}"
println "nwb_ecephys_args: ${params.nwb_ecephys_args}"
}


job_dispatch_to_preprocessing = channel.create()
ecephys_to_preprocessing = channel.fromPath(params.ecephys_path + "/", type: 'any')
Expand Down Expand Up @@ -238,7 +263,7 @@ process spikesort_kilosort25 {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-spikesort-kilosort25.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout c7b2d11ea0c258a0d07c28c105d365553ccfaf43 --quiet
git -C capsule-repo -c core.fileMode=false checkout 8c8987260a27c75b1f523d306b40a16962a97ea6 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -290,7 +315,7 @@ process spikesort_kilosort4 {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-spikesort-kilosort4.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout 2183dc930959c4e8007f7a8fbcc04f0fc72648ab --quiet
git -C capsule-repo -c core.fileMode=false checkout 6b4e6cd5bf90e05be7ce7e2de9a28f4dcfa02c29 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -339,7 +364,7 @@ process spikesort_spykingcircus2 {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-spikesort-spykingcircus2.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout 6f4ea112127d1727ba81040cf1563bcf9a40ca7d --quiet
git -C capsule-repo -c core.fileMode=false checkout 1f88d6741e33bf9a0e6e23107c64f3c7ad17b5e4 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -390,7 +415,7 @@ process postprocessing {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-postprocessing.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout f63b9b16c5ababd75826445f1f71a44298feeff2 --quiet
git -C capsule-repo -c core.fileMode=false checkout 1bcc57e0b6be45dc39afd3ef18e0ad678173cc2e --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -481,7 +506,7 @@ process unit_classifier {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-unit-classifier.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout 0231bdaa9cb1a812e55b0c938167049ba0ea62fe --quiet
git -C capsule-repo -c core.fileMode=false checkout a5f1e947c7099090cca2c8250b9bad0b796a67dd --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand All @@ -491,7 +516,7 @@ process unit_classifier {
echo "[${task.tag}] running capsule..."
cd capsule/code
chmod +x run
./run
./run ${params.unit_classifier_args}
echo "[${task.tag}] completed!"
"""
Expand Down Expand Up @@ -533,7 +558,7 @@ process visualization {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-visualization.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout bc4a6b7ed63624f7f1b280c0e23cf82cf330ae6a --quiet
git -C capsule-repo -c core.fileMode=false checkout f58ab7cda7757b4703da049a160a5677c2cd9c54 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down Expand Up @@ -589,7 +614,7 @@ process results_collector {
echo "[${task.tag}] cloning git repo..."
git clone "https://github.com/AllenNeuralDynamics/aind-ephys-results-collector.git" capsule-repo
git -C capsule-repo -c core.fileMode=false checkout dea3ac29ac8e82322b2a4488b56b6720861cc80a --quiet
git -C capsule-repo -c core.fileMode=false checkout 73cb90e9c321a6c06012681ca08d93b71e99d952 --quiet
mv capsule-repo/code capsule/code
rm -rf capsule-repo
Expand Down
3 changes: 3 additions & 0 deletions pipeline/nextflow_slurm.config
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,9 @@ process {

singularity {
enabled = true
autoMounts = true
singularity.enabled = true
singularity.autoMounts = true
platform = 'linux/amd64'
envWhitelist = ['KACHERY_ZONE', 'KACHERY_CLOUD_CLIENT_ID', 'KACHERY_CLOUD_PRIVATE_KEY']
}
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2 changes: 1 addition & 1 deletion pipeline/test_local.sh
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Expand Up @@ -6,4 +6,4 @@ fi

NXF_VER=22.10.8 DATA_PATH="$PWD/../sample_dataset/nwb/" RESULTS_PATH="$PWD/../sample_dataset/nwb_results/" \
nextflow -C nextflow_local.config -log $RESULTS_PATH/nextflow/nextflow.log run main_local.nf \
--sorter spykingcircus2 --job_dispatch_args "--input nwb" --preprocessing_args "--motion skip" $RESUME_FLAG
--sorter spykingcircus2 --runmode fast --job_dispatch_args "--input nwb" --preprocessing_args "--motion skip" $RESUME_FLAG

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