diff --git a/nextflow/modules/fecal_boli.nf b/nextflow/modules/fecal_boli.nf
index 503a759d..b1236a8a 100644
--- a/nextflow/modules/fecal_boli.nf
+++ b/nextflow/modules/fecal_boli.nf
@@ -1,3 +1,18 @@
+/**
+ * This module contains process definitions for fecal boli prediction and feature calculations.
+ */
+
+ /**
+ * Predicts fecal boli in the video at minute intervals.
+ *
+ * @param tuple
+ *  - video_file The input video file.
+ *  - in_pose The input pose file.
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with fecal boli predictions.
+ */
 process PREDICT_FECAL_BOLI {
     label "gpu"
     label "tracking"
@@ -16,6 +31,15 @@ process PREDICT_FECAL_BOLI {
     """
 }
 
+/**
+ * Extracts fecal boli features from the pose data.
+ *
+ * @param tuple
+ *  - video_file The input video file.
+ *  - in_pose The input pose file.
+ *
+ * @return fecal_boli The generated fecal boli feature CSV file.
+ */
 process EXTRACT_FECAL_BOLI_BINS {
     label "tracking"
     label "r_fboli_extract"
diff --git a/nextflow/modules/flexibility.nf b/nextflow/modules/flexibility.nf
index bbb3387f..3d73cfc2 100644
--- a/nextflow/modules/flexibility.nf
+++ b/nextflow/modules/flexibility.nf
@@ -1,3 +1,21 @@
+/**
+ * This module contains process definitions for generating flexibility metrics.
+ * These metrics were published in https://doi.org/10.1038/s43587-022-00266-0
+ */
+
+/**
+ * Generates flexibility index metrics from pose data.
+ *
+ * @param tuple
+ *  - video_file The input video file.
+ *  - pose_file The input pose file.
+ *
+ * @return tuple files
+ *  - Path to the generated angles CSV file.
+ *  - Path to the generated dAC CSV file.
+ *  - Path to the generated dB CSV file.
+ *  - Path to the generated flexdexraw CSV file.
+ */
 process GENERATE_FLEXIBILITY_INDEX {
     label "frailty"
     label "cpu"
@@ -32,6 +50,16 @@ process GENERATE_FLEXIBILITY_INDEX {
     """
 }
 
+/**
+ * Generates rear paw width metrics from pose data.
+ *
+ * @param tuple
+ *  - video_file The input video file.
+ *  - pose_file The input pose file.
+ *
+ * @return rearpaw Path to the generated rear paw width CSV file.
+ * @return rearpawsave Path to the generated rear paw save CSV file.
+ */
 process GENERATE_REAR_PAW_WIDTH {
     label "frailty"
     label "cpu"
diff --git a/nextflow/modules/gait.nf b/nextflow/modules/gait.nf
index 2e1f1300..c44cbd4a 100644
--- a/nextflow/modules/gait.nf
+++ b/nextflow/modules/gait.nf
@@ -1,3 +1,16 @@
+/**
+ * This module contains process definitions for gait analysis.
+ */
+
+/**
+ * Generates gait statistics from pose data.
+ *
+ * @param tuple
+ *  - video_file The input video file.
+ *  - pose_file The input pose file.
+ *
+ * @return gait_file The generated gait statistics file.
+ */
 process GENERATE_GAIT_H5 {
     label "gait"
     label "cpu"
@@ -24,7 +37,15 @@ process GENERATE_GAIT_H5 {
     """
 }
 
-
+/**
+ * Generates gait bin files from gait statistics.
+ *
+ * @param tuple
+ *  - gait_file The input gait statistics file.
+ *  - speed_bin The speed bin size for generating gait bins.
+ *
+ * @return gait_bin_csv The generated gait bin CSV file.
+ */
 process GENERATE_GAIT_BIN {
     label "gait"
     label "cpu"
diff --git a/nextflow/modules/jabs_classifiers.nf b/nextflow/modules/jabs_classifiers.nf
index af393c9e..c29607f4 100644
--- a/nextflow/modules/jabs_classifiers.nf
+++ b/nextflow/modules/jabs_classifiers.nf
@@ -1,3 +1,18 @@
+/**
+ * This module contains process definitions related to JABS classifiers.
+ */
+
+/**
+ * Calculates features for JABS classifiers.
+ *
+ * @param tuple
+ *  - video_file The input video file.
+ *  - in_pose The input pose file.
+ *
+ * @return tuple files
+ *  - Path to the original pose file.
+ *  - Path to the generated feature cache directory.
+ */
 process GENERATE_FEATURE_CACHE {
     // This process will correct pose pathing to a v6 file
     label "jabs_classify"
@@ -23,6 +38,20 @@ process GENERATE_FEATURE_CACHE {
     """
 }  
 
+/**
+ * Predicts behaviors using JABS classifiers.
+ *
+ * @param tuple
+ *  - in_pose The input pose file.
+ *  - feature_cache The directory containing the generated features.
+ * @param classifiers A map of classifiers:
+ *  - <classifier_name>: classifier parameter maps (not used by this process)
+ *
+ * @return tuple files
+ *  - Path to the original pose file.
+ *  - Path to the feature cache directory.
+ *  - Path to the generated behavior file. All behavior predictions are stored in a single file.
+ */
 process PREDICT_CLASSIFIERS {
     label "jabs_classify"
     label "cpu"
@@ -46,6 +75,22 @@ process PREDICT_CLASSIFIERS {
     """
 }
 
+/**
+ * Generates behavior tables from pose file, feature file, and prediction file.
+ *
+ * @param tuple
+ *  - in_pose The input pose file.
+ *  - feature_cache The directory containing the generated features.
+ *  - behavior_files The behavior prediction file.
+ * @param classifiers A map of classifiers:
+ *  - <classifier_name>: classifier parameter maps:
+ *    - stitch_value: the gap size for stitching behavior bouts
+ *    - filter_value: the minimum length for behavior bouts
+ *
+ * @return tuple files
+ *  - Path to the generated behavior bout file.
+ *  - Path to the generated behavior summary file.
+ */
 process GENERATE_BEHAVIOR_TABLES {
     label "jabs_postprocess"
     label "cpu"
@@ -53,18 +98,30 @@ process GENERATE_BEHAVIOR_TABLES {
 
     input:
     tuple path(in_pose), path(feature_cache), path(behavior_files)
-    val classifier
+    val classifiers
 
     output:
     tuple path("${in_pose.baseName}*_bouts.csv"), path("${in_pose.baseName}*_summaries.csv"), emit: files
 
     script:
     """
-    behavior_command="--behavior ${classifier.collect { entry -> "$entry.key --stitch_gap $entry.value.stitch_value --min_bout_length $entry.value.filter_value" }.join(' --behavior ')}"
+    behavior_command="--behavior ${classifiers.collect { entry -> "$entry.key --stitch_gap $entry.value.stitch_value --min_bout_length $entry.value.filter_value" }.join(' --behavior ')}"
     python3 /JABS-postprocess/generate_behavior_tables.py --project_folder . --feature_folder . --out_prefix ${in_pose.baseName} --out_bin_size 5 \${behavior_command}
     """
 }
 
+/**
+ * Generates heuristic classifier predictions.
+ *
+ * @param tuple
+ *  - in_pose The input pose file.
+ *  - feature_cache The directory containing the generated features.
+ * @param heuristic_classifiers A list of heuristic classifier configuration files.
+ *
+ * @return tuple files
+ *  - Path to the generated bout file.
+ *  - Path to the generated summary file.
+ */
 process PREDICT_HEURISTICS {
     label "jabs_postprocess"
     label "cpu"
@@ -87,6 +144,14 @@ process PREDICT_HEURISTICS {
     """
 }
 
+/**
+ * Converts a behavior summary table to features.
+ *
+ * @param in_summary_table The input behavior summary table.
+ * @param bin_size The bin size for feature extraction.
+ *
+ * @return features The generated feature file.
+ */
 process BEHAVIOR_TABLE_TO_FEATURES {
     label "jabs_table_convert"
     label "r_jabs_table_convert"
diff --git a/nextflow/modules/manual_correction.nf b/nextflow/modules/manual_correction.nf
index 745f51b2..6ee6c946 100644
--- a/nextflow/modules/manual_correction.nf
+++ b/nextflow/modules/manual_correction.nf
@@ -1,3 +1,17 @@
+/**
+ * This module contains process definitions related to manually correcting pose data using SLEAP.
+ */
+
+/**
+ * Extracts a frame from a video as a png image.
+ *
+ * @param tuple
+ *  - video The input video file.
+ *  - pose_file The input pose file (not used in this process).
+ * @param frame_index The index of the frame to extract.
+ *
+ * @return frame A png image of the extracted frame.
+ */
 process EXTRACT_VIDEO_FRAME {
     label "sleap"
 
@@ -14,6 +28,13 @@ process EXTRACT_VIDEO_FRAME {
     """
 }
 
+/**
+ * Adds a set of frames to a new SLEAP project file for arena corner annotation.
+ *
+ * @param video_frames A list of png images to be added to the SLEAP project.
+ *
+ * @return sleap_file The generated SLEAP project file containing the frames and arena corner skeleton for annotation.
+ */
 process ADD_EXAMPLES_TO_SLEAP {
     label "sleap"
 
@@ -48,6 +69,14 @@ process ADD_EXAMPLES_TO_SLEAP {
     """
 }
 
+/**
+ * Integrates SLEAP corner annotations into a pose file.
+ *
+ * @param pose_file The input pose file to be corrected.
+ * @param sleap_file The SLEAP project file containing the corner annotations.
+ *
+ * @return pose_file The corrected pose file with integrated corner annotations.
+ */
 process INTEGRATE_SLEAP_CORNER_ANNOTATIONS {
     label "sleap_io"
 
diff --git a/nextflow/modules/multi_mouse.nf b/nextflow/modules/multi_mouse.nf
index f8c155b9..4109b2c7 100644
--- a/nextflow/modules/multi_mouse.nf
+++ b/nextflow/modules/multi_mouse.nf
@@ -1,3 +1,14 @@
+/**
+ * Predicts multi-mouse segmentation.
+ *
+ * @param tuple
+ *  - video_file The input video file
+ *  - in_pose The input pose file
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with multi-mouse segmentation predicted.
+ */
 process PREDICT_MULTI_MOUSE_SEGMENTATION {
     label "gpu"
     label "tracking"
@@ -15,6 +26,17 @@ process PREDICT_MULTI_MOUSE_SEGMENTATION {
     """
 }
 
+/**
+ * Predicts multi-mouse keypoints.
+ *
+ * @param tuple
+ *  - video_file The input video file
+ *  - in_pose The input pose file
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with multi-mouse keypoints predicted.
+ */
 process PREDICT_MULTI_MOUSE_KEYPOINTS {
     label "gpu"
     label "tracking"
@@ -32,6 +54,17 @@ process PREDICT_MULTI_MOUSE_KEYPOINTS {
     """
 }
 
+/**
+ * Predicts multi-mouse identity.
+ *
+ * @param tuple
+ *  - video_file The input video file
+ *  - in_pose The input pose file
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with multi-mouse identity predicted.
+ */
 process PREDICT_MULTI_MOUSE_IDENTITY {
     label "gpu"
     label "tracking"
@@ -49,6 +82,18 @@ process PREDICT_MULTI_MOUSE_IDENTITY {
     """
 }
 
+/**
+ * Generates multi-mouse tracklets from the pose, segmentaiton, and identity data.
+ *
+ * @param tuple
+ *  - video_file The input video file
+ *  - in_pose The input pose file
+ *  - num_animals The number of animals to generate tracklets for
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with multi-mouse tracklets generated.
+ */
 process GENERATE_MULTI_MOUSE_TRACKLETS {
     label "cpu"
     label "tracking"
diff --git a/nextflow/modules/remote_io.nf b/nextflow/modules/remote_io.nf
index a0a4bae0..92cbf883 100644
--- a/nextflow/modules/remote_io.nf
+++ b/nextflow/modules/remote_io.nf
@@ -1,3 +1,14 @@
+/**
+ * This module contains process definitions for remote I/O operations.
+ */
+
+/**
+ * Checks if the user has a valid Globus authentication session.
+ *
+ * @param globus_endpoint The Globus endpoint to check authentication against
+ *
+ * @exception If the user is not authenticated, the process will exit with an error.
+ */
 process CHECK_GLOBUS_AUTH {
     label "globus"
     
@@ -21,6 +32,14 @@ process CHECK_GLOBUS_AUTH {
     // But this needs to be parsed and compared with the endpoint expiration
 }
 
+/**
+ * Filters a list of video files to only those that do not have corresponding processed pose files on Globus.
+ *
+ * @param globus_endpoint The Globus endpoint where processed pose files are stored
+ * @param test_files A file containing a list of video files to check
+ *
+ * @return unprocessed_files A file containing a list of video files that do not have a corresponding pose file.
+ */
 process FILTER_UNPROCESSED_GLOBUS {
     label "globus"
 
@@ -44,6 +63,14 @@ process FILTER_UNPROCESSED_GLOBUS {
     """
 }
 
+/**
+ * Filters a list of video files to only those that do not have corresponding processed pose files on Dropbox.
+ *
+ * @param dropbox_prefix The rclone remote prefix where processed pose files are stored
+ * @param test_files A file containing a list of video files to check
+ *
+ * @return unprocessed_files A file containing a list of video files that do not have corresponding processed pose files
+ */
 process FILTER_UNPROCESSED_DROPBOX {
     label "rclone"
     label "dropbox"
@@ -71,6 +98,15 @@ process FILTER_UNPROCESSED_DROPBOX {
     """
 }
 
+/**
+ * Transfers files between 2 Globus endpoints.
+ *
+ * @param globus_src_endpoint The source Globus endpoint to transfer files from
+ * @param globus_dst_endpoint The destination Globus endpoint to transfer files to
+ * @param files_to_transfer A file containing a list of files to transfer
+ *
+ * @return globus_folder A file containing the path to this tasks folder.
+ */
 process TRANSFER_GLOBUS {
     label "globus"
     
@@ -115,6 +151,14 @@ process TRANSFER_GLOBUS {
     """
 }
 
+/**
+ * Retrieves files from Dropbox using rclone.
+ *
+ * @param files_to_transfer A file containing a list of files to transfer
+ * @param dropbox_prefix The rclone remote prefix where files are stored
+ *
+ * @return remote_files A file containing a list of the retrieved files with full paths.
+ */
 process GET_DATA_FROM_DROPBOX {
     label "rclone"
     label "dropbox"
@@ -134,6 +178,15 @@ process GET_DATA_FROM_DROPBOX {
     """
 }
 
+/**
+ * Uploads a file to Dropbox using rclone.
+ *
+ * @param file_to_upload The file to be uploaded
+ * @param tuple
+ *  - result_file The path to the result file
+ *  - publish_filename The desired publish filename
+ * @param dropbox_prefix The rclone remote prefix where files are to be uploaded
+ */
 process PUT_DATA_TO_DROPBOX {
     label "rclone"
     label "dropbox"
diff --git a/nextflow/modules/single_mouse.nf b/nextflow/modules/single_mouse.nf
index ddc3940f..181a1c3f 100644
--- a/nextflow/modules/single_mouse.nf
+++ b/nextflow/modules/single_mouse.nf
@@ -1,3 +1,18 @@
+/**
+ * This module contains process definitions for single mouse pose estimation.
+ */
+
+/**
+ * Predicts single mouse segmentation using a pre-trained model.
+ *
+ * @param tuple
+ *  - video_file The input video file
+ *  - in_pose_file The input pose file
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with single mouse segmentation predicted.
+ */
 process PREDICT_SINGLE_MOUSE_SEGMENTATION {
     label "gpu"
     label "tracking"
@@ -16,6 +31,17 @@ process PREDICT_SINGLE_MOUSE_SEGMENTATION {
     """
 }
 
+/**
+ * Predicts single mouse keypoints using a pre-trained model.
+ *
+ * @param tuple
+ *  - video_file The input video file
+ *  - in_pose_file The input pose file
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with single mouse keypoints predicted.
+ */
 process PREDICT_SINGLE_MOUSE_KEYPOINTS {
     label "gpu"
     label "tracking"
@@ -34,6 +60,15 @@ process PREDICT_SINGLE_MOUSE_KEYPOINTS {
     """
 }
 
+/**
+ * Performs quality control on single mouse pose files.
+ *
+ * @param in_pose_file The input pose file to be checked
+ * @param clip_duration The duration of the video clip in seconds
+ * @param batch_name The name of the batch being processed
+ *
+ * @return qc_file The generated quality control CSV file
+ */
 process QC_SINGLE_MOUSE {
     label "tracking"
     label "r_single_qc"
@@ -55,6 +90,18 @@ process QC_SINGLE_MOUSE {
     """
 }
 
+/**
+ * Clips a video and its corresponding pose file to a specified duration from the start.
+ *
+ * @param tuple
+ *  - in_video The input video file to be clipped
+ *  - in_pose_file The input pose file to be clipped
+ * @param clip_duration The duration in frames to which the video and pose file should be clipped
+ *
+ * @return tuple files
+ *  - Path to the trimmed video file.
+ *  - Path to the trimmed pose file.
+ */
 process CLIP_VIDEO_AND_POSE {
     label "tracking"
     label "r_clip_video"
diff --git a/nextflow/modules/static_objects.nf b/nextflow/modules/static_objects.nf
index 21d30323..fce9700d 100644
--- a/nextflow/modules/static_objects.nf
+++ b/nextflow/modules/static_objects.nf
@@ -1,3 +1,18 @@
+/**
+ * This module contains process definitions for predicting static objects.
+ */
+
+/**
+ * Predicts arena corners.
+ *
+ * @param tuple
+ *  - video_file Path to the video file.
+ *  - in_pose Path to the input pose file.
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with arena corners predicted.
+ */
 process PREDICT_ARENA_CORNERS {
     label "gpu"
     label "tracking"
@@ -16,6 +31,17 @@ process PREDICT_ARENA_CORNERS {
     """
 }
 
+/*
+ * Predicts food hopper position.
+ *
+ * @param tuple
+ *  - video_file Path to the video file.
+ *  - in_pose Path to the input pose file.
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with food hopper predicted.
+ */
 process PREDICT_FOOD_HOPPER {
     label "gpu"
     label "tracking"
@@ -34,6 +60,17 @@ process PREDICT_FOOD_HOPPER {
     """
 }
 
+/**
+ * Predicts lixit position.
+ *
+ * @param tuple
+ *  - video_file Path to the video file.
+ *  - in_pose Path to the input pose file.
+ *
+ * @return tuple files
+ *  - Path to the original video file.
+ *  - Modified pose file with lixit predicted.
+ */
 process PREDICT_LIXIT {
     label "gpu"
     label "tracking"
diff --git a/nextflow/modules/utils.nf b/nextflow/modules/utils.nf
index 927a96d3..4ae0fc8e 100644
--- a/nextflow/modules/utils.nf
+++ b/nextflow/modules/utils.nf
@@ -1,9 +1,15 @@
+/**
+ * This module contains utility processes and functions for the Nextflow pipeline.
+ * It includes processes for file manipulation, data validation, and other utility functions.
+ */
+
 /**
  * Lazy nextflow module for creating files, useful for testing.
  *
  * @param file_name The name of the file to be created
  * @param file_content The content to be written to the file
- * @return A path to the created file
+ *
+ * @return created_file A path to the created file
  */
 process CREATE_FILE {
     label "r_util"
@@ -22,6 +28,15 @@ process CREATE_FILE {
     """
 }
 
+/**
+ * Filters a batch of files based on whether they exist, and optionally filters out already processed files.
+ *
+ * @param input_batch File containing a list of input files to be processed
+ * @param ignore_invalid_inputs If "true", process will not fail if a file does not exist. Will otherwise remove files that do not exist.
+ * @param filter_processed If "true", will filter out files that have already been processed
+ *
+ * @return process_filelist A file containing a filtered list of files to be processed
+ */
 process FILTER_LOCAL_BATCH {
     label "r_util"
 
@@ -38,9 +53,13 @@ process FILTER_LOCAL_BATCH {
     """
     touch files_to_process.txt
     while IFS="" read -r file; do
-        if [[ ! -f "\${file}" && ${ignore_invalid_inputs} != "true" ]]; then
-            echo "File does not exist: \${file}"
-            exit 1
+        if [[ ! -f "\${file}" ]]; then
+            if [[ ${ignore_invalid_inputs} != "true" ]]; then
+                echo "File does not exist: \${file}"
+                exit 1
+            else
+                echo "File does not exist: \${file}, skipping."
+            fi
         else
             echo "\${file} exists, adding to process list."
             echo "\${file}" >> files_to_process.txt
@@ -63,6 +82,15 @@ process FILTER_LOCAL_BATCH {
     """
 }
 
+/**
+ * Generates a dummy pose file for testing purposes.
+ *
+ * @param video_file The video file to create a pose file
+ *
+ * @return tuple files
+ *  - video_file input video file
+ *  - pose_file pose file
+ */
 process VIDEO_TO_POSE {
     label "r_util"
 
@@ -80,6 +108,14 @@ process VIDEO_TO_POSE {
     """
 }
 
+/**
+ * URLifies a file path to avoid potential file collisions in the pipeline.
+ *
+ * @param file_to_urlify The path to the file that needs to be URLified
+ * @param depth The number of directory levels to include in the URLified path
+ *
+ * @return file A path to the URLified file
+ */
 process URLIFY_FILE {
     label "r_util"
 
@@ -98,6 +134,13 @@ process URLIFY_FILE {
     """
 }
 
+/**
+ * Removes URLified fields from a file path.
+ *
+ * @param urlified_file The path to the URLified file that needs to be processed
+ *
+ * @return file A path to the file with URLified fields removed
+ */
 process REMOVE_URLIFY_FIELDS {
     label "r_util"
 
@@ -114,6 +157,15 @@ process REMOVE_URLIFY_FIELDS {
     """
 }
 
+/**
+ * Merges multiple feature files into a single CSV file by rows.
+ *
+ * @param feature_files A list of feature files to be merged
+ * @param out_filename The name of the output file
+ * @param header_size The number of header lines to keep from the first file
+ *
+ * @return merged_features The merged CSV file
+ */
 process MERGE_FEATURE_ROWS {
     label "r_util"
 
@@ -137,6 +189,15 @@ process MERGE_FEATURE_ROWS {
     """
 }
 
+/**
+ * Merges multiple feature files into a single CSV file by columns.
+ *
+ * @param feature_files A list of feature files to be merged
+ * @param col_to_merge_on The column name to merge the files on
+ * @param out_filename The name of the output file
+ *
+ * @return merged_features The merged CSV file
+ */
 process MERGE_FEATURE_COLS {
     // Any environment with pandas installed should work here.
     label "tracking"
@@ -164,6 +225,15 @@ process MERGE_FEATURE_COLS {
     """
 }
 
+/**
+ * Selects specific columns from a CSV file and outputs them to a new CSV file.
+ *
+ * @param qc_file The input CSV file
+ * @param key_1 The first column to select
+ * @param key_2 The second column to select
+ *
+ * @return csv_file A CSV file containing only the selected columns
+ */
 process SELECT_COLUMNS {
     label "r_util"
 
@@ -191,6 +261,15 @@ process SELECT_COLUMNS {
     """
 }
 
+/**
+ * Adds a new column to a CSV file with specified data. Typically used to add metadata columns.
+ *
+ * @param file_to_add_to The CSV file to which the column will be added
+ * @param column_name The name of the new column
+ * @param column_data The data to be added in the new column for all rows
+ *
+ * @return file A CSV file with the new column added
+ */
 process ADD_COLUMN {
     label "r_util"
 
@@ -209,6 +288,14 @@ process ADD_COLUMN {
     """
 }
 
+/**
+ * Deletes a specified row from a CSV file.
+ *
+ * @param file_to_delete_from The CSV file from which the row will be deleted
+ * @param row_to_delete The content of the row to be deleted (exact match)
+ *
+ * @return file A CSV file with the specified row removed
+ */
 process DELETE_ROW {
     label "r_util"
 
@@ -226,6 +313,14 @@ process DELETE_ROW {
     """
 }
 
+/**
+ * Converts a wide-format feature CSV file to a long-format CSV file.
+ *
+ * @param feature_file The input wide-format CSV file
+ * @param id_col The column to use as the identifier in the long format
+ *
+ * @return long_file A long-format CSV file
+ */
 process FEATURE_TO_LONG {
     // Any environment with pandas installed should work here.
     label "tracking"
@@ -249,6 +344,16 @@ process FEATURE_TO_LONG {
     """
 }
 
+/**
+ * Converts a long-format feature CSV file to a wide-format CSV file.
+ *
+ * @param long_file The input long-format CSV file
+ * @param id_col The column to use as the identifier in the wide format
+ * @param feature_col The column containing feature names
+ * @param value_col The column containing feature values
+ *
+ * @return wide_file A wide-format CSV file
+ */
 process LONG_TO_WIDE {
     // Any environment with pandas installed should work here.
     label "tracking"
@@ -274,28 +379,17 @@ process LONG_TO_WIDE {
     """
 }
 
-process SUBSET_PATH_BY_VAR {
-    label "r_util"
-
-    input:
-    path all_files
-    val subset_files
-    val dir
-
-    output:
-    path("${dir}/*"), emit: subset_files
-
-    script:
-    """
-    mkdir ${dir}
-    for file in ${subset_files}
-    do
-        ln -s \$(pwd)/\${file} ${dir}/\$(basename \${file})
-    done
-    sleep 10
-    """
-}
-
+/**
+ * Publishes a result file to a specified directory with potential sub-folders.
+ *
+ * @param tuple
+ *  - result_file The file to be published
+ *  - publish_filename The name under which the file will be published
+ *
+ * @return published_file A path to the published file
+ *
+ * @publish ./ File published to the specified directory
+ */
 process PUBLISH_RESULT_FILE {
     label "r_util"
 
@@ -319,6 +413,14 @@ process PUBLISH_RESULT_FILE {
     """
 }
 
+/**
+ * Obtains workflow version information and writes it to a file.
+ *
+ * @return version The workflow version
+ * @return version_file Path to the version file
+ *
+ * @publish ./ Workflow version information
+ */
 process GET_WORKFLOW_VERSION {
     label "r_util"
 
@@ -338,6 +440,16 @@ process GET_WORKFLOW_VERSION {
     """
 }
 
+/**
+ * Pairs a pose file with a generated video file.
+ *
+ * @param pose_file The pose file for which to create a video
+ * @param n_frames The number of frames the video should have
+ *
+ * @return tuple files
+ *  - video_file The created video file
+ *  - pose_file The input pose file
+ */
 process ADD_DUMMY_VIDEO {
     // Any environment with ffmpeg installed should work here.
     label "tracking"
@@ -361,6 +473,7 @@ process ADD_DUMMY_VIDEO {
  *
  * @param file_path The path to the file that needs validation
  * @param pipeline_type The type of pipeline being run (e.g. 'single-mouse', 'single-mouse-corrected-corners', etc.)
+ *
  * @return A boolean indicating if the file is valid and an error message if it's not
  */
 def validateInputFile(String file_path, String pipeline_type) {
@@ -392,6 +505,7 @@ def validateInputFile(String file_path, String pipeline_type) {
  *
  * @param in_file_list The path to the file that contains the list of intut files
  * @param pipeline_type The type of pipeline being run. See validateInputFile for valid types.
+ *
  * @return A list of valid file paths that match the allowed formats for the specified pipeline type.
  */
 def validateInputFilelist(String in_file_list, String pipeline_type) {
diff --git a/nextflow/workflows/feature_generation.nf b/nextflow/workflows/feature_generation.nf
index 1a4d055c..f3651273 100644
--- a/nextflow/workflows/feature_generation.nf
+++ b/nextflow/workflows/feature_generation.nf
@@ -1,3 +1,6 @@
+/**
+ * This module contains workflows related to feature generation from pose files.
+ */
 include { GENERATE_GAIT_H5; GENERATE_GAIT_BIN } from "${projectDir}/nextflow/modules/gait"
 include { GENERATE_FLEXIBILITY_INDEX; GENERATE_REAR_PAW_WIDTH } from "${projectDir}/nextflow/modules/flexibility"
 include { GET_WORKFLOW_VERSION;
@@ -32,6 +35,20 @@ include { GENERATE_FEATURE_CACHE;
           BEHAVIOR_TABLE_TO_FEATURES } from "${projectDir}/nextflow/modules/jabs_classifiers"
 include { EXTRACT_FECAL_BOLI_BINS } from "${projectDir}/nextflow/modules/fecal_boli"
 
+/**
+ * Workflow to generate features from single mouse pose v2 files.
+ * Generates gait and morphometric feature sets.
+ *
+ * @param tuple input_pose_v2_batch
+ *  - Path to the input video file.
+ *  - Path to the corresponding pose v2 file.
+ *
+ * @return path gait_results The channel of generated gait feature files.
+ * @return path morphometrics_results The channel of generated morphometric feature files.
+ *
+ * @publish ./results/ Gait feature files
+ * @publish ./results/ Morphometric feature files
+ */
 workflow SINGLE_MOUSE_V2_FEATURES {
     take:
     // tuple of video_file and pose_file from SINGLE_MOUSE_TRACKING
@@ -74,6 +91,20 @@ workflow SINGLE_MOUSE_V2_FEATURES {
     morphometrics_results
 }
 
+/**
+ * Workflow to generate JABS features from single mouse pose v6 files.
+ * Generates heuristic and classifier-based behavior features, as well as fecal boli counts.
+ *
+ * @param tuple input_pose_v6_batch
+ *  - Path to the input video file.
+ *  - Path to the corresponding pose v6 file.
+ *
+ * @return path wide_jabs_features The channel of generated JABS feature files.
+ * @return path fecal_boli_table The channel of generated fecal boli count files.
+ *
+ * @publish ./results/ JABS feature files
+ * @publish ./results/ Fecal boli count files
+ */
 workflow SINGLE_MOUSE_V6_FEATURES {
     take:
     // tuple of video_file and pose_file from SINGLE_MOUSE_TRACKING
diff --git a/nextflow/workflows/io.nf b/nextflow/workflows/io.nf
index 693fb2be..a121c966 100644
--- a/nextflow/workflows/io.nf
+++ b/nextflow/workflows/io.nf
@@ -1,3 +1,7 @@
+/**
+ * This module contains workflows that manipulate inputs and outputs to pipelines.
+ */
+ 
 include { FILTER_LOCAL_BATCH;
           URLIFY_FILE;
           validateInputFile;
@@ -9,6 +13,19 @@ include { CHECK_GLOBUS_AUTH;
           GET_DATA_FROM_DROPBOX;
         } from "${projectDir}/nextflow/modules/remote_io"
 
+/**
+ * Prepares data for the main pipeline. Steps include:
+ * - Validating input files by extension
+ * - [Optional] Filtering of already processed files
+ * - Retrieval of files if remote
+ * - URLifying file names to avoid collisions
+ *
+ * @param path in_video_file Text file containing list of files to process. One file per line.
+ * @param val location The location of the input files (local, dropbox, or globus).
+ * @param val skip_urlify If true, skips the URLification step. Some usages may already have URLified files.
+ *
+ * @return path file_processing_channel The channel containing the prepared input files.
+ */
 workflow PREPARE_DATA {
     take:
     in_video_file
diff --git a/nextflow/workflows/multi_mouse_pipeline.nf b/nextflow/workflows/multi_mouse_pipeline.nf
index 9c71d7f3..8ed447f6 100644
--- a/nextflow/workflows/multi_mouse_pipeline.nf
+++ b/nextflow/workflows/multi_mouse_pipeline.nf
@@ -1,3 +1,7 @@
+/**
+ * This module contains the multi-mouse tracking pipeline.
+ * It processes video input to track multiple mice, predict their poses, and identify static objects.
+ */
 include { PREDICT_MULTI_MOUSE_SEGMENTATION;
           PREDICT_MULTI_MOUSE_KEYPOINTS;
           PREDICT_MULTI_MOUSE_IDENTITY;
@@ -11,6 +15,18 @@ include { VIDEO_TO_POSE;
           PUBLISH_RESULT_FILE as PUBLISH_MM_POSE_V6;
  } from "${projectDir}/nextflow/modules/utils"
 
+/**
+ * Main workflow for predicting multimouse poses from video input.
+ *
+ * @param path input_video The input video file to process.
+ * @param val num_animals The number of animals to track in the video.
+ *
+ * @return tuple pose_v6
+ *  - Path to the input video file.
+ *  - Path to the pose v6 file produced.
+ *
+ * @publish ./results/ Pose v6 results
+ */
 workflow MULTI_MOUSE_TRACKING {
     take:
     input_video
diff --git a/nextflow/workflows/single_mouse_pipeline.nf b/nextflow/workflows/single_mouse_pipeline.nf
index 676762b2..26ce03f1 100644
--- a/nextflow/workflows/single_mouse_pipeline.nf
+++ b/nextflow/workflows/single_mouse_pipeline.nf
@@ -1,3 +1,7 @@
+/**
+ * This module contains the single mouse tracking pipeline.
+ * It processes video input to track a single mouse.
+ */
 include { PREDICT_SINGLE_MOUSE_SEGMENTATION; PREDICT_SINGLE_MOUSE_KEYPOINTS; CLIP_VIDEO_AND_POSE } from "${projectDir}/nextflow/modules/single_mouse"
 include { PREDICT_ARENA_CORNERS } from "${projectDir}/nextflow/modules/static_objects"
 include { PREDICT_FECAL_BOLI } from "${projectDir}/nextflow/modules/fecal_boli"
@@ -14,6 +18,21 @@ include { VIDEO_TO_POSE;
           PUBLISH_RESULT_FILE as PUBLISH_SM_POSE_V6_NOCORN;
  } from "${projectDir}/nextflow/modules/utils"
 
+/**
+ * Main workflow for single mouse tracking.
+ *
+ * @param path input_video The input video file to process.
+ *
+ * @return tuple pose_v2_data
+ *  - Path to the input video file.
+ *  - Path to the pose v2 file produced.
+ * @return tuple pose_v6_data
+ *  - Path to the input video file.
+ *  - Path to the pose v6 file produced.
+ *
+ * @publish ./results/ Trimmed video files
+ * @publish ./results/ Single mouse pose v2 results
+ */
 workflow SINGLE_MOUSE_TRACKING {
     take:
     input_video
@@ -46,6 +65,26 @@ workflow SINGLE_MOUSE_TRACKING {
     pose_v6_data
 }
 
+/**
+ * Workflow to split pose files based on whether corners were detected.
+ * If corners are missing, the pose file is sent for manual correction.
+ * Default files are provided if either channel in the split is empty.
+ *
+ * @param tuple input_pose_v6_batch
+ *  - Path to the input video file.
+ *  - Path to the pose v6 file produced.
+ *
+ * @return tuple v6_with_corners
+ *  - Path to the input video file.
+ *  - Path to the pose v6 file with corners present.
+ * @return tuple v6_without_corners
+ *  - Path to the input video file.
+ *  - Path to the pose v6 file without corners present.
+ *
+ * @publish ./ Single mouse quality control results
+ * @publish ./results/ Single mouse pose v6 results with corners
+ * @publish ./failed_corners/ Single mouse pose v6 results without corners. Files are url-ified.
+ */
 workflow SPLIT_BY_CORNERS {
     take:
     input_pose_v6_batch
diff --git a/nextflow/workflows/sleap_manual_correction.nf b/nextflow/workflows/sleap_manual_correction.nf
index 8560a4e3..6654a8e7 100644
--- a/nextflow/workflows/sleap_manual_correction.nf
+++ b/nextflow/workflows/sleap_manual_correction.nf
@@ -1,6 +1,19 @@
+/**
+ * This module contains workflows for manual correction of arena corner annotations.
+ */
 include { EXTRACT_VIDEO_FRAME; ADD_EXAMPLES_TO_SLEAP; INTEGRATE_SLEAP_CORNER_ANNOTATIONS } from "${projectDir}/nextflow/modules/manual_correction"
 include { PUBLISH_RESULT_FILE as PUBLISH_SM_MANUAL_CORRECT } from "${projectDir}/nextflow/modules/utils"
 
+/**
+ * Workflow to generate a SLEAP file for manual correction of arena corners.
+ *
+ * @param path input_files Channel of input video files to extract frames from.
+ * @param val frame_index The index of the frame to extract from each video.
+ *
+ * @return path sleap_file The SLEAP file containing the extracted frames for manual correction.
+ *
+ * @publish ./ Manual corner correction SLEAP file
+ */
 workflow MANUALLY_CORRECT_CORNERS {
     take:
     input_files
@@ -18,6 +31,14 @@ workflow MANUALLY_CORRECT_CORNERS {
     sleap_file
 }
 
+/**
+ * Workflow to integrate manually corrected corner annotations from a SLEAP file back into pose files.
+ *
+ * @param path pose_files Channel of pose files to update with corrected corner annotations.
+ * @param path sleap_file The SLEAP file containing the manually corrected corner annotations.
+ *
+ * @return path corrected_poses The channel of pose files updated with the corrected corner annotations.
+ */
 workflow INTEGRATE_CORNER_ANNOTATIONS {
     take:
     pose_files