diff --git a/.github/workflows/build-processing.yaml b/.github/workflows/build-processing.yaml
new file mode 100644
index 0000000..6870ba0
--- /dev/null
+++ b/.github/workflows/build-processing.yaml
@@ -0,0 +1,57 @@
+name: Build Processing Image
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - '*'
+    paths:
+      - 'processing/**'
+  pull_request:
+    branches:
+      - main
+    paths:
+      - 'processing/**'
+
+env:
+  REGISTRY: ghcr.io
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+
+    - name: Login to GitHub Container Registry
+      uses: docker/login-action@v3
+      with:
+        registry: ${{ env.REGISTRY }}
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Extract metadata (tags, labels) for processing container
+      id: meta-processing
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.REGISTRY }}/${{ github.repository }}/processing
+        flavor: latest=false
+        tags: |
+          type=ref,event=branch
+          type=ref,event=pr
+          type=sha,prefix=main-
+          type=semver,pattern={{version}}
+          type=semver,pattern={{major}}.{{minor}}
+
+    - name: Build and push processing container image
+      uses: docker/build-push-action@v5
+      with:
+        context: ./processing
+        file: ./processing/dockerfile
+        push: true
+        tags: ${{ steps.meta-processing.outputs.tags }}
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diff --git a/processing/dockerfile b/processing/dockerfile
new file mode 100644
index 0000000..9a08ab4
--- /dev/null
+++ b/processing/dockerfile
@@ -0,0 +1,31 @@
+FROM rocker/r-ver:4.3.3
+
+WORKDIR /home/docker/
+
+# Library initialization using renv
+RUN Rscript --vanilla -e " \
+  options(repos = c(CRAN = 'https://cloud.r-project.org')); \
+  install.packages('renv') \
+"
+
+# Direct dependencies
+RUN Rscript --vanilla -e " \
+  renv::install( \
+    packages = c( \
+      'dplyr@1.1.4', \
+      'magrittr@2.0.3', \
+      'optparse@1.7.5', \
+      'readr@2.1.5', \
+      'renv@1.0.7', \
+      'stringr@1.5.1', \
+      'tidyr@1.3.1' \
+    ), \
+    prompt = F, \
+    lock = T \
+  ) \
+"
+# Data processing code
+COPY process.R /home/docker/
+
+# Run container
+ENTRYPOINT ["Rscript", "--vanilla", "process.R"]
\ No newline at end of file
diff --git a/processing/process.R b/processing/process.R
new file mode 100644
index 0000000..53025c5
--- /dev/null
+++ b/processing/process.R
@@ -0,0 +1,372 @@
+##############
+# Parameters #
+##############
+
+library(optparse)
+
+logger = function(..., sep = ""){
+  cat("\n", format(Sys.time(), format = '%Y-%m-%d %H:%M:%S'), " ", ..., sep = sep)}
+
+strwrap2 = function(x, lw = 80){
+  gsub("\\s{2,}", " ", x) |>
+  strwrap(width = lw, simplify = T) |>
+  paste(collapse = "\n")}
+
+parser = OptionParser(
+  option_list = list(
+    
+    make_option(
+      opt_str = c("-i", "--input"),
+      help = strwrap2(
+        "Input file, in CSV format containing at minimum columns: sampleDate,
+        siteName, mN1, mN2, mFluA, mFluB, and mBiomarker."),
+      type = "character",
+      default = ""),
+
+    make_option(
+      opt_str = c("-w", "--weights"),
+      help = strwrap2(
+        "Input file, in CSV format with columns: Site, and Weight. The site 
+        column corresponds to siteName values in the input file. Weights
+        represents factor used for combing site-specific trends into a single 
+        regional trend. Weights are decimal numbers and should sum to 1.
+        The weights may be set to be equal, or correspond to population
+        weighting, sampling frequency, or any other user-determined criteria."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-p", "--patch"),
+      help = strwrap2(
+        "Input file, in CSV format with columns: Date, Site, and one or more of 
+        mN1, mN2, mFluA, mFluB, mBiomarker. Values in the patch file will add or
+        overide any existing values in the primary input file."),
+      type = "character",
+      default = ""),
+  
+    make_option(
+      opt_str = c("-C", "--output_region_covid"),
+      help = strwrap2(
+        "Output location for CSV file containing regional summary for 
+        SARS-CoV-2. No output will be generated if left blank."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-A", "--output_region_flu_a"),
+      help = strwrap2(
+        "Output location for CSV file containing regional summary for 
+        Influenza A. No output will be generated if left blank."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-B", "--output_region_flu_b"),
+      help = strwrap2(
+        "Output location for CSV file containing regional summary for 
+        Influenza B. No output will be generated if left blank."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-c", "--output_covid"),
+      help = strwrap2(
+        "Output location for CSV file containing site-specific SARS-CoV-2 data.
+        No output will be generated if left blank."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-a", "--output_flu_a"),
+      help = strwrap2(
+        "Output location for CSV file containing site-specific Influenza A data.
+        No output will be generated if left blank."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-b", "--output_flu_b"),
+      help = strwrap2(
+        "Output location for CSV file containing site-specific Influenza B data.
+        No output will be generated if left blank."),
+      type = "character",
+      default = ""),
+    
+    make_option(
+      opt_str = c("-v", "--verbose"),
+      help = strwrap2(
+        "Print additional diagnostic information."),
+      action = "store_true",
+      default = FALSE)
+    )
+  )
+
+# Parse arguments
+args = parse_args(parser)
+
+# Verbose argument
+if(args$verbose){
+  logger("The following arguments have been passed to R:",
+    commandArgs(trailingOnly = TRUE))
+  }
+
+
+###################
+# Data processing #
+###################
+
+# Warn of package conflicts only in verbose mode
+options(conflicts.policy = list("warn" = args$verbose))
+
+library(readr)
+library(dplyr)
+
+# Note on variable prefixes:
+# n: biomarker-normalized
+# r: relative
+# s: kernel-smoothed
+# d: derivative/slope (with respect to date)
+
+ww = read_csv(
+  file = args$input,
+  show_col_types = F,
+  progress = F,
+  col_types = cols_only(
+    sampleDate = col_date(format = "%m/%d/%Y"),
+    siteName   = col_character(),
+    mN1        = col_double(),
+    mN2        = col_double(),
+    mFluA      = col_double(),
+    mFluB      = col_double(),
+    mBiomarker = col_double())) |>
+  suppressMessages() |>
+  rename(
+    "Date"  = sampleDate,
+    "Site"  = siteName)
+
+# Patch file application
+if(args$patch != ""){
+  logger("Applying patch file")
+  
+  ww = merge(
+    x = ww,
+    y = read_csv(
+      file = args$patch,
+      show_col_types = F,
+      progress = F), 
+    all = T,
+    by = c("Site", "Date"),
+    suffixes = c("", ".patch")) |>
+    
+    mutate(
+      across(
+        .cols = ends_with(".patch"),
+        .fns = \(x) coalesce(get(sub(".patch$", "", cur_column())), x),
+        .names = "{sub('.patch$', '', .col)}")) |>
+    select(-ends_with(".patch"))
+  }
+
+  # Biomarker-normalize values
+  ww = ww |>
+  mutate(
+    across(
+      .cols = c(mN1, mN2, mFluA, mFluB),
+      .names = "n{.col}",
+      .fns = \(x){x / mBiomarker}
+    )
+  ) |>
+  
+  # Scale N1 and N2 to max values within each sewershed,
+  # representing signal between 0 and 1.
+  group_by(Site) |>
+  mutate(
+    
+    # Cap values at 95th percentile
+    across(
+      .cols = where(is.numeric),
+      .fns = \(x) {
+        DescTools::Winsorize(x, probs = c(0, 0.95), na.rm = T)}),
+    
+    # Scale values [0, 1]
+    across(
+      .cols = where(is.numeric),
+      .fns = \(x) {x/max(x, na.rm = T)})) |>
+  ungroup() |>
+  
+  # Rename to reflected scaled (relative) values
+  rename(
+    "rN1"        = "mN1",
+    "rN2"        = "mN2",
+    "rFluA"      = "mFluA",
+    "rFluB"      = "mFluB",
+    "rnN1"       = "nmN1",
+    "rnN2"       = "nmN2",
+    "rnFluA"     = "nmFluA",
+    "rnFluB"     = "nmFluB",
+    "rBiomarker" = "mBiomarker") |>
+  
+  # Combine N1 and N2 data for SARS-CoV-2
+  rowwise() |>
+  mutate(
+    rN1N2 = mean(c(rN1, rN2), na.rm = T),
+    rnN1N2 = mean(c(rnN1, rnN2), na.rm = T),) |>
+  ungroup()
+
+
+###############
+# Site Trends #
+###############
+
+# Create a tidier `ksmooth()`
+ksmooth2 = function(date, y, kernel, bandwidth){
+  # Data must be sorted and free of NAs to ksmooth
+  data = data.frame(date, y) |>
+    arrange(date) |>
+    na.omit()
+  
+  # Use complete `Date` for fitted values
+  ksmooth(
+    x = data$date, y = data$y,
+    kernel = kernel,
+    bandwidth = bandwidth,
+    x.points = date) |>
+    magrittr::use_series(y)
+  }
+
+ww_ks = ww |>
+  
+  # Ensure coverage of all dates
+  right_join(
+    expand.grid(
+      "Date" = seq.Date(
+        from = min(ww$Date, na.rm = T),
+        to = max(ww$Date, na.rm = T),
+        by = "1 day"),
+      "Site" = unique(ww$Site)),
+    by = c("Date", "Site"),
+    relationship = "one-to-one",
+    unmatched = "error") |>
+  
+  # Site specific trends
+  group_by(Site) |>
+  arrange(Date) |>
+  mutate(
+    across(
+      .cols = c(
+        rN1N2, rFluA, rFluB,
+        rnN1N2, rnFluA, rnFluB),
+      .names = "s{.col}",
+      .fns = \(x) ksmooth2(
+        date = Date,
+        y = x,
+        kernel = "normal",
+        bandwidth = 21)
+      )
+    ) |>
+  ungroup()
+
+
+##############
+# Site Files # 
+##############
+
+# COVID
+if(args$output_covid != "") {
+  logger("Preparing sewershed-specific COVID output")
+  
+  ww_ks |>
+    select(Date, Site, ends_with("N1N2")) |> 
+    filter(!is.na(srN1N2)) |>
+    write_csv(file = args$output_covid)}
+
+# Influenza A
+if(args$output_flu_a != "") {
+  logger("Preparing sewershed-specific Influenza A output")
+  
+  ww_ks |>
+    select(Date, Site, ends_with("FluA")) |> 
+    filter(!is.na(srFluA)) |>
+    write_csv(file = args$output_flu_a)}
+
+# Influenza B
+if(args$output_flu_b != "") {
+  logger("Preparing sewershed-specific Influenza B output")
+  
+  ww_ks |>
+    select(Date, Site, ends_with("FluB")) |> 
+    filter(!is.na(srFluB)) |>
+    write_csv(file = args$output_flu_b)}
+
+##################S
+# Regional Trend #
+##################
+
+# Read in weights file
+weights = read_csv(
+  file = args$weights,
+  show_col_types = F,
+  progress = F,
+  col_types = cols_only(
+    Site = col_character(),
+    Weight = col_double()))
+
+  ww_regional = ww_ks |>
+  select(
+    Date,
+    Site,
+    # Kernel Smoothed, Relative measurements
+    starts_with("sr")) |>
+
+  # Add site weights
+  inner_join(
+    y = weights,
+    by = c("Site"),
+    relationship = "many-to-one",
+    unmatched = "error") |>
+  
+  # Apply weights
+  mutate(
+    across(
+      .cols = starts_with("sr"),
+      .fns = \(x){x * Weight})) |>
+
+  # Combine signals
+  group_by(Date) |>
+  summarize(across(
+    .cols = starts_with("sr"),
+    .fns = \(x) sum(x, na.rm = F)),
+    .groups = "drop")
+
+
+##################
+# Regional Files #
+##################
+
+# COVID
+if(args$output_region_covid != "") {
+  logger("Preparing regional COVID output")
+  
+  ww_regional |>
+    select(Date, ends_with("N1N2")) |>
+    filter(!is.na(srN1N2)) |>
+    write_csv(file = args$output_region_covid)}
+
+# Influenza A
+if(args$output_region_flu_a != "") {
+  logger("Preparing regional Influenza A output")
+  
+  ww_regional |>
+    select(Date, ends_with("FluA")) |>
+    filter(!is.na(srFluA)) |>
+    write_csv(file = args$output_region_flu_a)}
+
+# Influenza B
+if(args$output_region_flu_b != "") {
+  logger("Preparing regional Influenza B output")
+  
+  ww_regional |>
+    select(Date, ends_with("FluB")) |>
+    filter(!is.na(srFluB)) |>
+    write_csv(file = args$output_region_flu_b)}
+    
+logger("Done!")
\ No newline at end of file