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‎.github/workflows/params_test_custom.json‎

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"preprocessing": {
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"job_kwargs": {
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"chunk_duration": "1s",
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"progress_bar": false
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"progress_bar": false,
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"mp_context": "spawn"
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},
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"min_preprocessing_duration": 120,
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"custom_preprocessing_pipeline": {},
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"denoising_strategy": "cmr",
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"filter_type": "bandpass",
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"highpass_filter": {
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"freq_min": 300.0,
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"margin_ms": 5.0
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},
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"bandpass_filter": {
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"freq_min": 300.0,
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"freq_max": 6000.0,
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"margin_ms": 5.0
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},
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"phase_shift": {
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"margin_ms": 100.0
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},
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"detect_bad_channels": {
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"method": "coherence+psd",
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"dead_channel_threshold": -0.5,
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"noisy_channel_threshold": 1.0,
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"outside_channel_threshold": -0.3,
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"outside_channels_location": "top",
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"n_neighbors": 11,
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"seed": 0
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},
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"remove_out_channels": true,
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"remove_bad_channels": true,
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"remove_out_channels": false,
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"remove_bad_channels": false,
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"max_bad_channel_fraction": 0.5,
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"common_reference": {
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"reference": "global",
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"operator": "median"
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},
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"highpass_spatial_filter": {
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"n_channel_pad": 60,
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"n_channel_taper": null,
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"direction": "y",
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"apply_agc": true,
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"agc_window_length_s": 0.01,
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"highpass_butter_order": 3,
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"highpass_butter_wn": 0.01
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"denoising_strategy": "destripe",
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"default_preprocessing_pipeline": {
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"phase_shift": {
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"margin_ms": 100.0
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},
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"highpass_filter": {
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"freq_min": 300.0,
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"margin_ms": 5.0
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},
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"bandpass_filter": {
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"freq_min": 300.0,
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"freq_max": 6000.0,
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"margin_ms": 5.0
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},
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"detect_and_remove_bad_channels": {
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"method": "coherence+psd",
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"dead_channel_threshold": -0.5,
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"noisy_channel_threshold": 1.0,
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"outside_channel_threshold": -0.3,
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"outside_channels_location": "top",
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"n_neighbors": 11,
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"channel_filters": ["noise", "dead", "out"],
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"seed": 0
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},
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"common_reference": {
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"reference": "global",
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"operator": "median"
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},
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"highpass_spatial_filter": {
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"n_channel_pad": 10,
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"n_channel_taper": null,
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"direction": "y",
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"apply_agc": true,
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"agc_window_length_s": 0.01,
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"highpass_butter_order": 3,
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"highpass_butter_wn": 0.01
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}
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},
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"custom_preprocessing_pipeline": null,
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"motion_correction": {
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"compute": false,
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"apply": false,
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"preset": "dredge_fast",
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"detect_kwargs": {},
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"select_kwargs": {},

.github/workflows/params_test.json renamed to .github/workflows/params_test_default.json

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"preprocessing": {
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"job_kwargs": {
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"chunk_duration": "1s",
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"progress_bar": false
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},
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"min_preprocessing_duration": 120,
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"custom_preprocessing_pipeline": null,
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"denoising_strategy": "cmr",
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"filter_type": "bandpass",
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"highpass_filter": {
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"freq_min": 300.0,
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"margin_ms": 5.0
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},
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"bandpass_filter": {
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"freq_min": 300.0,
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"freq_max": 6000.0,
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"margin_ms": 5.0
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},
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"phase_shift": {
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"margin_ms": 100.0
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},
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"detect_bad_channels": {
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"method": "coherence+psd",
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"dead_channel_threshold": -0.5,
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"noisy_channel_threshold": 1.0,
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"outside_channel_threshold": -0.3,
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"outside_channels_location": "top",
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"n_neighbors": 11,
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"seed": 0
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"progress_bar": false,
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"mp_context": "spawn"
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},
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"filter_type": "highpass",
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"remove_out_channels": true,
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"remove_bad_channels": true,
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"max_bad_channel_fraction": 0.5,
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"common_reference": {
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"reference": "global",
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"operator": "median"
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},
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"highpass_spatial_filter": {
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"n_channel_pad": 60,
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"n_channel_taper": null,
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"direction": "y",
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"apply_agc": true,
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"agc_window_length_s": 0.01,
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"highpass_butter_order": 3,
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"highpass_butter_wn": 0.01
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"denoising_strategy": "cmr",
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"default_preprocessing_pipeline": {
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"phase_shift": {
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"margin_ms": 100.0
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},
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"highpass_filter": {
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"freq_min": 300.0,
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"margin_ms": 5.0
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},
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"bandpass_filter": {
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"freq_min": 300.0,
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"freq_max": 6000.0,
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"margin_ms": 5.0
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},
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"detect_and_remove_bad_channels": {
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"method": "coherence+psd",
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"dead_channel_threshold": -0.5,
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"noisy_channel_threshold": 1.0,
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"outside_channel_threshold": -0.3,
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"outside_channels_location": "top",
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"n_neighbors": 11,
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"channel_filters": ["noise", "dead", "out"],
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"seed": 0
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},
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"common_reference": {
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"reference": "global",
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"operator": "median"
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},
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"highpass_spatial_filter": {
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"n_channel_pad": 10,
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"n_channel_taper": null,
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"direction": "y",
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"apply_agc": true,
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"agc_window_length_s": 0.01,
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"highpass_butter_order": 3,
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"highpass_butter_wn": 0.01
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}
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},
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"custom_preprocessing_pipeline": null,
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"motion_correction": {
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"compute": true,
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"apply": false,
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"preset": "dredge_fast",
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"detect_kwargs": {},
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"select_kwargs": {},

‎.github/workflows/test_pipeline.yml‎

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This file was deleted.

‎.github/workflows/test_pipeline_custom.yml‎

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pull_request:
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branches: [main]
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types: [synchronize, opened, reopened]
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env:
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NXF_SYNTAX_PARSER: v1
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jobs:
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test:
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runs-on: ubuntu-latest

‎.gitignore‎

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# User-specific files
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pipeline/nextflow_slurm_custom.config
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pipeline/capsule_versions_custom.env
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*.idea
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.idea
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.claude

‎docs/source/troubleshooting.rst‎

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If you encounter a problem not listed here, please consider opening an issue on our GitHub repository.
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ERROR ~ Script compilation failed
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---------------------------------
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The most recent versions of nextflow (v26.04.0) made some `strict syntax <https://docs.seqera.io/nextflow/strict-syntax>`_
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the default for nextflow scripts, causing the error ``Script compilation failed`` when running the pipeline.
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While we resolve the compatibility issues with the new syntax, you can set the environment variable
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``NXF_SYNTAX_PARSER`` to ``v1`` to use the previous syntax parser:
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.. note::
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To make these changes persistent, you can add the following lines to your ``.bashrc`` or ``.bash_profile`` file:
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.. code-block:: bash
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export NXF_SYNTAX_PARSER=v1
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NUMBA cache issue: ``RuntimeError: cannot cache function``
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----------------------------------------------------------
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`nextflow_slurm.config <https://github.com/AllenNeuralDynamics/aind-ephys-pipeline/blob/main/pipeline/nextflow_slurm.config#L120>`_
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file, so they will be automatically used automatically if defined.
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.. note.::
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This error should not happen anymore with the latest versions of the containers, which do not run as root.
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See `this PR <https://github.com/AllenNeuralDynamics/aind-ephys-pipeline/pull/103>`_ for more details.
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``OSError: Read-only file system`` error
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----------------------------------------
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// containerOptions = "--bind \$HOME:\$HOME"
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.. note.::
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This error should not happen anymore with the latest versions of the containers, which do not run as root.
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See `this PR <https://github.com/AllenNeuralDynamics/aind-ephys-pipeline/pull/103>`_ for more details.
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``OSError: Unable to synchronously open file``
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----------------------------------------------

‎tests/params_test.json‎

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"progress_bar": false,
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"mp_context": "spawn"
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},
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"filter_type": "bandpass",
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"remove_out_channels": false,
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"remove_bad_channels": false,
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"filter_type": "highpass",
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"remove_out_channels": true,
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"remove_bad_channels": true,
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"max_bad_channel_fraction": 0.5,
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"denoising_strategy": "destripe",
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"denoising_strategy": "cmr",
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"default_preprocessing_pipeline": {
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"phase_shift": {
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"margin_ms": 100.0

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