diff --git a/.gitignore b/.gitignore
index 1210604..b08956c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -117,6 +117,9 @@ poetry.lock
 **/.nextflow
 **/*.log*
 
+# Metaflow metadata
+**/.metaflow
+
 # notebooks
 **/*.ipynb
 
diff --git a/README.md b/README.md
index 2d8d41d..c20bfe2 100644
--- a/README.md
+++ b/README.md
@@ -3,31 +3,103 @@
 
 ## Setup
 
-Swap the path in `envs/env.yaml` to the project root to your cloned path:
+### Environment Setup
+
+Install the project and workflow environment:
+
+```bash
+# project environment with Metaflow
+conda env create --name <name> --file envs/env.yaml
+```
+
+Update the path in `envs/env.yaml` to point to your cloned repository path:
 
 ```yaml
 ...
   - pip:
-    # swap me for git URL
+    # swap me for git URL or local path
     - /path/to/cloned/repo
 ...
 ```
 
-Install the nextflow and project environments:
+### Configuration
+
+If running on Gemini, ensure that Alphafold MSAs will use your scratch as a tmp directory (some MSA intermediate files are larger than `/tmp` on compute nodes).
+
+Configure Metaflow if needed:
 
 ```bash
-# project environment
-conda env create --name <name> --file envs/env.yaml
-# nf-core/nextflow env 
-conda env create --name <name> --file envs/nf-core.yaml
+# Optional: configure Metaflow datastore location
+export METAFLOW_DATASTORE_SYSROOT_LOCAL=/path/to/datastore
 ```
 
-If running on Gemini, ensure that Alphafold MSAs will use your scratch as a tmp directory (some MSA intermediate files are larger than `/tmp` on compute nodes)
+## Workflows
+
+This project uses **Metaflow** for workflow orchestration. The workflows have been migrated from the previous Nextflow implementation.
+
+### Running Workflows
+
+#### Command Line Usage
 
 ```bash
-vim ~/.nextflow/config
+cd workflows
+python linear_epitope_flow.py run --dset-name <dataset> --workflow-type <type>
 ```
 
+Where `<dataset>` can be:
+- `bp3c50id`
+- `hv_class` 
+- `hv_seg`
+- `iedb_bp3`
+- `in_class`
+- `in_seg`
+
+And `<type>` can be:
+- `clean`: Data cleaning and preparation
+- `msa_focal`: MSA generation for focal proteins
+- `msa_peptide`: MSA generation for peptides  
+- `inference_focal`: AlphaFold3 inference for focal proteins
+- `inference_peptide`: AlphaFold3 inference for peptides
+- `bepipred`: BepiPred scoring
+- `extract_conf`: Confidence extraction
+
+#### SLURM Job Submission
+
+Use the provided shell scripts to submit jobs to SLURM:
+
 ```bash
-params.msa_tmpdir = "/scratch/<username>/tmp"
-```
\ No newline at end of file
+# Clean raw data
+sbatch scripts_metaflow/bp3c50id/00_run_clean_raw_data.sh
+
+# Run MSA for focal proteins
+sbatch scripts_metaflow/bp3c50id/02_run_msa_focal_protein.sh
+
+# Run inference
+sbatch scripts_metaflow/bp3c50id/03_run_inference_focal_protein.sh
+
+# Run BepiPred
+sbatch scripts_metaflow/bp3c50id/04_run_bepipred.sh
+
+# Extract confidence
+sbatch scripts_metaflow/bp3c50id/06_extract_conf.sh
+```
+
+#### Pipeline Execution Order
+
+For a complete analysis, run workflows in this order:
+
+1. **Clean raw data** (`clean`)
+2. **Generate MSA** (`msa_focal` or `msa_peptide`)  
+3. **Run inference** (`inference_focal` or `inference_peptide`)
+4. **Calculate BepiPred scores** (`bepipred`)
+5. **Extract confidence** (`extract_conf`)
+
+### Legacy Nextflow Files
+
+The old Nextflow workflows have been replaced with Metaflow. For reference, the original files are still present in the `workflows/` directory but are no longer used:
+
+- `*.nf` files - Original Nextflow workflow definitions
+- `scripts/` - Original Nextflow execution scripts  
+- `nextflow.config` - Nextflow configuration
+
+For current usage, use the Metaflow workflows described above.
\ No newline at end of file
diff --git a/envs/DEPRECATED_nf-core.md b/envs/DEPRECATED_nf-core.md
new file mode 100644
index 0000000..92af2a3
--- /dev/null
+++ b/envs/DEPRECATED_nf-core.md
@@ -0,0 +1,8 @@
+# DEPRECATED: nf-core environment
+
+This file is deprecated and no longer needed.
+
+The Nextflow/nf-core environment has been replaced with Metaflow.
+All dependencies are now included in the main `env.yaml` file.
+
+Use `env.yaml` instead of this file.
\ No newline at end of file
diff --git a/envs/env.yaml b/envs/env.yaml
index ab47790..fa6a607 100644
--- a/envs/env.yaml
+++ b/envs/env.yaml
@@ -29,7 +29,11 @@ dependencies:
   # viz
   - py3Dmol
 
+  # workflow orchestration
+  - pip
+  
   - pip:
     # swap me for git URL
     - -e /tgen_labs/altin/alphafold3/runs/linear_peptide
     - git+https://github.com/ljwoods2/mdaf3.git@main
+    - metaflow
diff --git a/envs/nf-core.yaml b/envs/nf-core.yaml.deprecated
similarity index 100%
rename from envs/nf-core.yaml
rename to envs/nf-core.yaml.deprecated
diff --git a/scripts/DEPRECATED_NEXTFLOW.md b/scripts/DEPRECATED_NEXTFLOW.md
new file mode 100644
index 0000000..8e54b38
--- /dev/null
+++ b/scripts/DEPRECATED_NEXTFLOW.md
@@ -0,0 +1,22 @@
+# DEPRECATED: Nextflow Execution Scripts
+
+**⚠️ NOTICE: These Nextflow execution scripts have been replaced with Metaflow scripts.**
+
+This directory contains the original shell scripts that launched Nextflow workflows. They are no longer actively used and have been replaced with Metaflow-based execution scripts.
+
+## Migration Information
+
+- **Old system**: Shell scripts in this directory that run `nextflow run`
+- **New system**: Shell scripts in `scripts_metaflow/` that run `python linear_epitope_flow.py run`
+- **Migration date**: July 2025
+
+## For Current Usage
+
+Please use the new Metaflow execution scripts instead:
+
+```bash
+# Use scripts in scripts_metaflow/ directory
+sbatch scripts_metaflow/bp3c50id/00_run_clean_raw_data.sh
+```
+
+See the main README.md for complete usage instructions.
\ No newline at end of file
diff --git a/scripts_metaflow/bp3c50id/00_run_clean_raw_data.sh b/scripts_metaflow/bp3c50id/00_run_clean_raw_data.sh
new file mode 100755
index 0000000..0ef004d
--- /dev/null
+++ b/scripts_metaflow/bp3c50id/00_run_clean_raw_data.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=clean_raw_data
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/bp3c50id/clean_raw_data.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/bp3c50id
+
+# Run Metaflow workflow for data cleaning
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name bp3c50id \
+    --workflow-type clean
\ No newline at end of file
diff --git a/scripts_metaflow/bp3c50id/02_run_msa_focal_protein.sh b/scripts_metaflow/bp3c50id/02_run_msa_focal_protein.sh
new file mode 100755
index 0000000..38f0426
--- /dev/null
+++ b/scripts_metaflow/bp3c50id/02_run_msa_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=msa_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/bp3c50id/focal_protein/msa.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/bp3c50id/focal_protein
+
+# Run Metaflow workflow for MSA focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name bp3c50id \
+    --workflow-type msa_focal
\ No newline at end of file
diff --git a/scripts_metaflow/bp3c50id/03_run_inference_focal_protein.sh b/scripts_metaflow/bp3c50id/03_run_inference_focal_protein.sh
new file mode 100755
index 0000000..b4b3a71
--- /dev/null
+++ b/scripts_metaflow/bp3c50id/03_run_inference_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=inference_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/bp3c50id/focal_protein/inference.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/bp3c50id/focal_protein
+
+# Run Metaflow workflow for inference focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name bp3c50id \
+    --workflow-type inference_focal
\ No newline at end of file
diff --git a/scripts_metaflow/bp3c50id/04_run_bepipred.sh b/scripts_metaflow/bp3c50id/04_run_bepipred.sh
new file mode 100755
index 0000000..ad7b88a
--- /dev/null
+++ b/scripts_metaflow/bp3c50id/04_run_bepipred.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=bepipred
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 8
+#SBATCH --time=2-00:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --output=tmp/metaflow/bp3c50id/focal_protein/bepipred.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/bp3c50id/focal_protein
+
+# Run Metaflow workflow for BepiPred
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name bp3c50id \
+    --workflow-type bepipred
\ No newline at end of file
diff --git a/scripts_metaflow/bp3c50id/06_extract_conf.sh b/scripts_metaflow/bp3c50id/06_extract_conf.sh
new file mode 100755
index 0000000..dd27612
--- /dev/null
+++ b/scripts_metaflow/bp3c50id/06_extract_conf.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=extract_conf
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/bp3c50id/focal_protein/extract_conf.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/bp3c50id/focal_protein
+
+# Run Metaflow workflow for confidence extraction
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name bp3c50id \
+    --workflow-type extract_conf
\ No newline at end of file
diff --git a/scripts_metaflow/hv_class/00_run_clean_raw_data.sh b/scripts_metaflow/hv_class/00_run_clean_raw_data.sh
new file mode 100755
index 0000000..25d1cf9
--- /dev/null
+++ b/scripts_metaflow/hv_class/00_run_clean_raw_data.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=clean_raw_data
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/hv_class/clean_raw_data.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_class
+
+# Run Metaflow workflow for data cleaning
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_class \
+    --workflow-type clean
\ No newline at end of file
diff --git a/scripts_metaflow/hv_class/02_run_msa_focal_protein.sh b/scripts_metaflow/hv_class/02_run_msa_focal_protein.sh
new file mode 100755
index 0000000..a221209
--- /dev/null
+++ b/scripts_metaflow/hv_class/02_run_msa_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=msa_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/hv_class/focal_protein/msa.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_class/focal_protein
+
+# Run Metaflow workflow for MSA focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_class \
+    --workflow-type msa_focal
\ No newline at end of file
diff --git a/scripts_metaflow/hv_class/03_run_inference_focal_protein.sh b/scripts_metaflow/hv_class/03_run_inference_focal_protein.sh
new file mode 100755
index 0000000..a801af1
--- /dev/null
+++ b/scripts_metaflow/hv_class/03_run_inference_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=inference_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/hv_class/focal_protein/inference.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_class/focal_protein
+
+# Run Metaflow workflow for inference focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_class \
+    --workflow-type inference_focal
\ No newline at end of file
diff --git a/scripts_metaflow/hv_class/04_run_bepipred.sh b/scripts_metaflow/hv_class/04_run_bepipred.sh
new file mode 100755
index 0000000..b7e2310
--- /dev/null
+++ b/scripts_metaflow/hv_class/04_run_bepipred.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=bepipred
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 8
+#SBATCH --time=2-00:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --output=tmp/metaflow/hv_class/focal_protein/bepipred.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_class/focal_protein
+
+# Run Metaflow workflow for BepiPred
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_class \
+    --workflow-type bepipred
\ No newline at end of file
diff --git a/scripts_metaflow/hv_class/06_extract_conf.sh b/scripts_metaflow/hv_class/06_extract_conf.sh
new file mode 100755
index 0000000..cc97ab4
--- /dev/null
+++ b/scripts_metaflow/hv_class/06_extract_conf.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=extract_conf
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/hv_class/focal_protein/extract_conf.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_class/focal_protein
+
+# Run Metaflow workflow for confidence extraction
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_class \
+    --workflow-type extract_conf
\ No newline at end of file
diff --git a/scripts_metaflow/hv_seg/00_run_clean_raw_data.sh b/scripts_metaflow/hv_seg/00_run_clean_raw_data.sh
new file mode 100755
index 0000000..be0c3b1
--- /dev/null
+++ b/scripts_metaflow/hv_seg/00_run_clean_raw_data.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=clean_raw_data
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/hv_seg/clean_raw_data.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_seg
+
+# Run Metaflow workflow for data cleaning
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_seg \
+    --workflow-type clean
\ No newline at end of file
diff --git a/scripts_metaflow/hv_seg/02_run_msa_focal_protein.sh b/scripts_metaflow/hv_seg/02_run_msa_focal_protein.sh
new file mode 100755
index 0000000..487b7e7
--- /dev/null
+++ b/scripts_metaflow/hv_seg/02_run_msa_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=msa_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/hv_seg/focal_protein/msa.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_seg/focal_protein
+
+# Run Metaflow workflow for MSA focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_seg \
+    --workflow-type msa_focal
\ No newline at end of file
diff --git a/scripts_metaflow/hv_seg/03_run_inference_focal_protein.sh b/scripts_metaflow/hv_seg/03_run_inference_focal_protein.sh
new file mode 100755
index 0000000..34633a1
--- /dev/null
+++ b/scripts_metaflow/hv_seg/03_run_inference_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=inference_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/hv_seg/focal_protein/inference.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_seg/focal_protein
+
+# Run Metaflow workflow for inference focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_seg \
+    --workflow-type inference_focal
\ No newline at end of file
diff --git a/scripts_metaflow/hv_seg/04_run_bepipred.sh b/scripts_metaflow/hv_seg/04_run_bepipred.sh
new file mode 100755
index 0000000..aee5670
--- /dev/null
+++ b/scripts_metaflow/hv_seg/04_run_bepipred.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=bepipred
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 8
+#SBATCH --time=2-00:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --output=tmp/metaflow/hv_seg/focal_protein/bepipred.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_seg/focal_protein
+
+# Run Metaflow workflow for BepiPred
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_seg \
+    --workflow-type bepipred
\ No newline at end of file
diff --git a/scripts_metaflow/hv_seg/06_extract_conf.sh b/scripts_metaflow/hv_seg/06_extract_conf.sh
new file mode 100755
index 0000000..013a6c5
--- /dev/null
+++ b/scripts_metaflow/hv_seg/06_extract_conf.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=extract_conf
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/hv_seg/focal_protein/extract_conf.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/hv_seg/focal_protein
+
+# Run Metaflow workflow for confidence extraction
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name hv_seg \
+    --workflow-type extract_conf
\ No newline at end of file
diff --git a/scripts_metaflow/iedb_bp3/00_run_clean_raw_data.sh b/scripts_metaflow/iedb_bp3/00_run_clean_raw_data.sh
new file mode 100755
index 0000000..73e0cfa
--- /dev/null
+++ b/scripts_metaflow/iedb_bp3/00_run_clean_raw_data.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=clean_raw_data
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/iedb_bp3/clean_raw_data.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/iedb_bp3
+
+# Run Metaflow workflow for data cleaning
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name iedb_bp3 \
+    --workflow-type clean
\ No newline at end of file
diff --git a/scripts_metaflow/iedb_bp3/02_run_msa_focal_protein.sh b/scripts_metaflow/iedb_bp3/02_run_msa_focal_protein.sh
new file mode 100755
index 0000000..e2433c7
--- /dev/null
+++ b/scripts_metaflow/iedb_bp3/02_run_msa_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=msa_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/iedb_bp3/focal_protein/msa.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/iedb_bp3/focal_protein
+
+# Run Metaflow workflow for MSA focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name iedb_bp3 \
+    --workflow-type msa_focal
\ No newline at end of file
diff --git a/scripts_metaflow/iedb_bp3/03_run_inference_focal_protein.sh b/scripts_metaflow/iedb_bp3/03_run_inference_focal_protein.sh
new file mode 100755
index 0000000..ec4d840
--- /dev/null
+++ b/scripts_metaflow/iedb_bp3/03_run_inference_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=inference_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/iedb_bp3/focal_protein/inference.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/iedb_bp3/focal_protein
+
+# Run Metaflow workflow for inference focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name iedb_bp3 \
+    --workflow-type inference_focal
\ No newline at end of file
diff --git a/scripts_metaflow/iedb_bp3/04_run_bepipred.sh b/scripts_metaflow/iedb_bp3/04_run_bepipred.sh
new file mode 100755
index 0000000..0510bb6
--- /dev/null
+++ b/scripts_metaflow/iedb_bp3/04_run_bepipred.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=bepipred
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 8
+#SBATCH --time=2-00:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --output=tmp/metaflow/iedb_bp3/focal_protein/bepipred.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/iedb_bp3/focal_protein
+
+# Run Metaflow workflow for BepiPred
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name iedb_bp3 \
+    --workflow-type bepipred
\ No newline at end of file
diff --git a/scripts_metaflow/iedb_bp3/06_extract_conf.sh b/scripts_metaflow/iedb_bp3/06_extract_conf.sh
new file mode 100755
index 0000000..ab88294
--- /dev/null
+++ b/scripts_metaflow/iedb_bp3/06_extract_conf.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=extract_conf
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/iedb_bp3/focal_protein/extract_conf.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/iedb_bp3/focal_protein
+
+# Run Metaflow workflow for confidence extraction
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name iedb_bp3 \
+    --workflow-type extract_conf
\ No newline at end of file
diff --git a/scripts_metaflow/in_class/00_run_clean_raw_data.sh b/scripts_metaflow/in_class/00_run_clean_raw_data.sh
new file mode 100755
index 0000000..3c77bfe
--- /dev/null
+++ b/scripts_metaflow/in_class/00_run_clean_raw_data.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=clean_raw_data
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/in_class/clean_raw_data.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_class
+
+# Run Metaflow workflow for data cleaning
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_class \
+    --workflow-type clean
\ No newline at end of file
diff --git a/scripts_metaflow/in_class/02_run_msa_focal_protein.sh b/scripts_metaflow/in_class/02_run_msa_focal_protein.sh
new file mode 100755
index 0000000..e28fae2
--- /dev/null
+++ b/scripts_metaflow/in_class/02_run_msa_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=msa_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/in_class/focal_protein/msa.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_class/focal_protein
+
+# Run Metaflow workflow for MSA focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_class \
+    --workflow-type msa_focal
\ No newline at end of file
diff --git a/scripts_metaflow/in_class/03_run_inference_focal_protein.sh b/scripts_metaflow/in_class/03_run_inference_focal_protein.sh
new file mode 100755
index 0000000..0a6df9a
--- /dev/null
+++ b/scripts_metaflow/in_class/03_run_inference_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=inference_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/in_class/focal_protein/inference.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_class/focal_protein
+
+# Run Metaflow workflow for inference focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_class \
+    --workflow-type inference_focal
\ No newline at end of file
diff --git a/scripts_metaflow/in_class/04_run_bepipred.sh b/scripts_metaflow/in_class/04_run_bepipred.sh
new file mode 100755
index 0000000..43447a7
--- /dev/null
+++ b/scripts_metaflow/in_class/04_run_bepipred.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=bepipred
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 8
+#SBATCH --time=2-00:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --output=tmp/metaflow/in_class/focal_protein/bepipred.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_class/focal_protein
+
+# Run Metaflow workflow for BepiPred
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_class \
+    --workflow-type bepipred
\ No newline at end of file
diff --git a/scripts_metaflow/in_class/06_extract_conf.sh b/scripts_metaflow/in_class/06_extract_conf.sh
new file mode 100755
index 0000000..aeb6f49
--- /dev/null
+++ b/scripts_metaflow/in_class/06_extract_conf.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=extract_conf
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/in_class/focal_protein/extract_conf.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_class/focal_protein
+
+# Run Metaflow workflow for confidence extraction
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_class \
+    --workflow-type extract_conf
\ No newline at end of file
diff --git a/scripts_metaflow/in_seg/00_run_clean_raw_data.sh b/scripts_metaflow/in_seg/00_run_clean_raw_data.sh
new file mode 100755
index 0000000..d435abd
--- /dev/null
+++ b/scripts_metaflow/in_seg/00_run_clean_raw_data.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=clean_raw_data
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/in_seg/clean_raw_data.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_seg
+
+# Run Metaflow workflow for data cleaning
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_seg \
+    --workflow-type clean
\ No newline at end of file
diff --git a/scripts_metaflow/in_seg/02_run_msa_focal_protein.sh b/scripts_metaflow/in_seg/02_run_msa_focal_protein.sh
new file mode 100755
index 0000000..14f37e7
--- /dev/null
+++ b/scripts_metaflow/in_seg/02_run_msa_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=msa_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/in_seg/focal_protein/msa.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_seg/focal_protein
+
+# Run Metaflow workflow for MSA focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_seg \
+    --workflow-type msa_focal
\ No newline at end of file
diff --git a/scripts_metaflow/in_seg/03_run_inference_focal_protein.sh b/scripts_metaflow/in_seg/03_run_inference_focal_protein.sh
new file mode 100755
index 0000000..5050290
--- /dev/null
+++ b/scripts_metaflow/in_seg/03_run_inference_focal_protein.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=inference_focal_protein
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH --time=5-00:00:00
+#SBATCH -c 16
+#SBATCH --output=tmp/metaflow/in_seg/focal_protein/inference.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_seg/focal_protein
+
+# Run Metaflow workflow for inference focal protein
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_seg \
+    --workflow-type inference_focal
\ No newline at end of file
diff --git a/scripts_metaflow/in_seg/04_run_bepipred.sh b/scripts_metaflow/in_seg/04_run_bepipred.sh
new file mode 100755
index 0000000..4e73c68
--- /dev/null
+++ b/scripts_metaflow/in_seg/04_run_bepipred.sh
@@ -0,0 +1,19 @@
+#!/bin/bash
+#SBATCH --job-name=bepipred
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 8
+#SBATCH --time=2-00:00:00
+#SBATCH --gres=gpu:1
+#SBATCH --output=tmp/metaflow/in_seg/focal_protein/bepipred.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_seg/focal_protein
+
+# Run Metaflow workflow for BepiPred
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_seg \
+    --workflow-type bepipred
\ No newline at end of file
diff --git a/scripts_metaflow/in_seg/06_extract_conf.sh b/scripts_metaflow/in_seg/06_extract_conf.sh
new file mode 100755
index 0000000..c825bb8
--- /dev/null
+++ b/scripts_metaflow/in_seg/06_extract_conf.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+#SBATCH --job-name=extract_conf
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=lwoods@tgen.org
+#SBATCH --ntasks=1
+#SBATCH --mem=64G
+#SBATCH -c 1
+#SBATCH --time=1:00:00
+#SBATCH --output=tmp/metaflow/in_seg/focal_protein/extract_conf.%j.log
+
+# Create log directory
+mkdir -p tmp/metaflow/in_seg/focal_protein
+
+# Run Metaflow workflow for confidence extraction
+cd workflows
+python linear_epitope_flow.py run \
+    --dset-name in_seg \
+    --workflow-type extract_conf
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_meta/_self.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_meta/_self.json
new file mode 100644
index 0000000..409ece5
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_meta/_self.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858336}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.DONE.lock b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.DONE.lock
new file mode 100644
index 0000000..3cc762b
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.DONE.lock
@@ -0,0 +1 @@
+""
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.attempt.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.attempt.json
new file mode 100644
index 0000000..e074f4d
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.attempt.json
@@ -0,0 +1 @@
+{"time": 1753295858.3394258}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.data.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.data.json
new file mode 100644
index 0000000..00fdb77
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/0.data.json
@@ -0,0 +1 @@
+{"datastore": "local", "version": "1.0", "attempt": 0, "python_version": "3.12.3 (main, Jun 18 2025, 17:59:45) [GCC 13.3.0]", "objects": {"workflow_type": "b2ddf3a31c01a4e0d3635e8e9a4d8fa39b34ab44", "torch_home": "e8254d917411fc7ee4ae3955315088f05af0ca9c", "name": "f30302c78b37e1b1886f5f78fe5949bb2e7b7d2d", "esm_dir": "1303ac1fe66ac7a6e6bdaca7025726e8e37ace78", "dset_name": "a3e35cafb680ed64677624f3f2e189e5c844bec1", "data_dir": "05179022ab0c1b0fa4a988a57130f835974ac950", "_transition": "dbc1aaddc8b7343d6d33b34edcf608b8f8801918", "_task_ok": "868436778cb011a1c6230bc12534683ab0b7f1c3", "_success": "868436778cb011a1c6230bc12534683ab0b7f1c3", "_graph_info": "fc762fe1515f741d9c013b1633011b6160b63a2c", "_foreach_stack": "c5cf38908fc549f499ade5b17ce221ff0ced377f", "_configs_processed": "868436778cb011a1c6230bc12534683ab0b7f1c3"}, "info": {"workflow_type": {"size": 20, "type": "<class 'str'>", "encoding": "gzip+pickle-v4"}, "torch_home": {"size": 37, "type": "<class 'str'>", "encoding": "gzip+pickle-v4"}, "name": {"size": 32, "type": "<class 'str'>", "encoding": "gzip+pickle-v4"}, "esm_dir": {"size": 45, "type": "<class 'str'>", "encoding": "gzip+pickle-v4"}, "dset_name": {"size": 19, "type": "<class 'str'>", "encoding": "gzip+pickle-v4"}, "data_dir": {"size": 19, "type": "<class 'str'>", "encoding": "gzip+pickle-v4"}, "_transition": {"size": 4, "type": "<class 'NoneType'>", "encoding": "gzip+pickle-v4"}, "_task_ok": {"size": 4, "type": "<class 'bool'>", "encoding": "gzip+pickle-v4"}, "_success": {"size": 4, "type": "<class 'bool'>", "encoding": "gzip+pickle-v4"}, "_graph_info": {"size": 840, "type": "<class 'dict'>", "encoding": "gzip+pickle-v4"}, "_foreach_stack": {"size": 5, "type": "<class 'list'>", "encoding": "gzip+pickle-v4"}, "_configs_processed": {"size": 4, "type": "<class 'bool'>", "encoding": "gzip+pickle-v4"}}}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__configs_processed.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__configs_processed.json
new file mode 100644
index 0000000..6239186
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__configs_processed.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "step_name": "_parameters", "task_id": "0", "attempt_id": 0, "name": "_configs_processed", "content_type": "gzip+pickle-v4", "type": "metaflow.artifact", "sha": "868436778cb011a1c6230bc12534683ab0b7f1c3", "ds_type": "local", "location": ":root:/home/runner/work/af3-linear-epitopes/af3-linear-epitopes/workflows/.metaflow", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858344}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__foreach_stack.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__foreach_stack.json
new file mode 100644
index 0000000..04c4a9c
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__foreach_stack.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "step_name": "_parameters", "task_id": "0", "attempt_id": 0, "name": "_foreach_stack", "content_type": "gzip+pickle-v4", "type": "metaflow.artifact", "sha": "c5cf38908fc549f499ade5b17ce221ff0ced377f", "ds_type": "local", "location": ":root:/home/runner/work/af3-linear-epitopes/af3-linear-epitopes/workflows/.metaflow", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858344}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__graph_info.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__graph_info.json
new file mode 100644
index 0000000..d0aa03c
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__graph_info.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "step_name": "_parameters", "task_id": "0", "attempt_id": 0, "name": "_graph_info", "content_type": "gzip+pickle-v4", "type": "metaflow.artifact", "sha": "fc762fe1515f741d9c013b1633011b6160b63a2c", "ds_type": "local", "location": ":root:/home/runner/work/af3-linear-epitopes/af3-linear-epitopes/workflows/.metaflow", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858344}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__success.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__success.json
new file mode 100644
index 0000000..3228419
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__success.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "step_name": "_parameters", "task_id": "0", "attempt_id": 0, "name": "_success", "content_type": "gzip+pickle-v4", "type": "metaflow.artifact", "sha": "868436778cb011a1c6230bc12534683ab0b7f1c3", "ds_type": "local", "location": ":root:/home/runner/work/af3-linear-epitopes/af3-linear-epitopes/workflows/.metaflow", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858344}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__task_ok.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__task_ok.json
new file mode 100644
index 0000000..b8b4b80
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__task_ok.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "step_name": "_parameters", "task_id": "0", "attempt_id": 0, "name": "_task_ok", "content_type": "gzip+pickle-v4", "type": "metaflow.artifact", "sha": "868436778cb011a1c6230bc12534683ab0b7f1c3", "ds_type": "local", "location": ":root:/home/runner/work/af3-linear-epitopes/af3-linear-epitopes/workflows/.metaflow", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858344}
\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__transition.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__transition.json
new file mode 100644
index 0000000..0137d51
--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact__transition.json
@@ -0,0 +1 @@
+{"run_number": "1753295858334854", "step_name": "_parameters", "task_id": "0", "attempt_id": 0, "name": "_transition", "content_type": "gzip+pickle-v4", "type": "metaflow.artifact", "sha": "dbc1aaddc8b7343d6d33b34edcf608b8f8801918", "ds_type": "local", "location": ":root:/home/runner/work/af3-linear-epitopes/af3-linear-epitopes/workflows/.metaflow", "flow_id": "LinearEpitopeFlow", "user_name": "runner", "tags": [], "system_tags": ["metaflow_version:2.16.5", "user:runner", "runtime:dev", "python_version:3.12.3"], "ts_epoch": 1753295858343}
\ No newline at end of file
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact_esm_dir.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact_esm_dir.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact_name.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact_name.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact_torch_home.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/_parameters/0/_meta/0_artifact_torch_home.json
new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.DONE.lock b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.DONE.lock
new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.data.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.data.json
new file mode 100644
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--- /dev/null
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.runtime b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.runtime
new file mode 100644
index 0000000..f6fb0a8
--- /dev/null
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.task_begin b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/0.task_begin
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact__current_step.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact__current_step.json
new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact__foreach_stack.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact__foreach_stack.json
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact_data_dir.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact_data_dir.json
new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact_torch_home.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/0_artifact_torch_home.json
new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/_self.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/_self.json
new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/sysmeta_attempt_1753295858540.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/sysmeta_attempt_1753295858540.json
new file mode 100644
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--- /dev/null
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/sysmeta_git-info_1753295858347.json b/workflows/.metaflow/LinearEpitopeFlow/1753295858334854/start/1/_meta/sysmeta_git-info_1753295858347.json
new file mode 100644
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@@ -0,0 +1 @@
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/0_artifact_esm_dir.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/0_artifact_esm_dir.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/0_artifact_name.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/0_artifact_name.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/0_artifact_torch_home.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/0_artifact_torch_home.json
new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/sysmeta_python_version_1753295868941.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/_parameters/0/_meta/sysmeta_python_version_1753295868941.json
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new file mode 100644
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new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/0.data.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/0.data.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/0.runtime b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/0.runtime
new file mode 100644
index 0000000..f6fb0a8
--- /dev/null
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/0.task_begin b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/0.task_begin
new file mode 100644
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new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__current_step.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__current_step.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__exception.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__exception.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__foreach_num_splits.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__foreach_num_splits.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__foreach_stack.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__foreach_stack.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__foreach_var.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__foreach_var.json
new file mode 100644
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new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__success.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__success.json
new file mode 100644
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new file mode 100644
index 0000000..6698f47
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__transition.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact__transition.json
new file mode 100644
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--- /dev/null
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@@ -0,0 +1 @@
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_base_path.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_base_path.json
new file mode 100644
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--- /dev/null
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_data_dir.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_data_dir.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_dset_name.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_dset_name.json
new file mode 100644
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_esm_dir.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_esm_dir.json
new file mode 100644
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@@ -0,0 +1 @@
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_name.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_name.json
new file mode 100644
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new file mode 100644
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--- /dev/null
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_torch_home.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_torch_home.json
new file mode 100644
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@@ -0,0 +1 @@
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_workflow_type.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/0_artifact_workflow_type.json
new file mode 100644
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\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/_self.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/_self.json
new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_attempt-done_1753295869147.json
@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_attempt_1753295869140.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_attempt_1753295869140.json
new file mode 100644
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--- /dev/null
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new file mode 100644
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--- /dev/null
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_ds-root_1753295869140.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_ds-root_1753295869140.json
new file mode 100644
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--- /dev/null
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\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_ds-type_1753295869140.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_ds-type_1753295869140.json
new file mode 100644
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--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_git-info_1753295868949.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_git-info_1753295868949.json
new file mode 100644
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--- /dev/null
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@@ -0,0 +1 @@
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\ No newline at end of file
diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_git-info_1753295869138.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_git-info_1753295869138.json
new file mode 100644
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--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_git-info_1753295869138.json
@@ -0,0 +1 @@
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_metaflow_version_1753295868949.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_metaflow_version_1753295868949.json
new file mode 100644
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--- /dev/null
+++ b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_metaflow_version_1753295868949.json
@@ -0,0 +1 @@
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diff --git a/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_metaflow_version_1753295869138.json b/workflows/.metaflow/LinearEpitopeFlow/1753295868939043/start/1/_meta/sysmeta_metaflow_version_1753295869138.json
new file mode 100644
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--- /dev/null
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diff --git a/workflows/DEPRECATED_NEXTFLOW.md b/workflows/DEPRECATED_NEXTFLOW.md
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+++ b/workflows/DEPRECATED_NEXTFLOW.md
@@ -0,0 +1,36 @@
+# DEPRECATED: Nextflow Workflows
+
+**⚠️ NOTICE: These Nextflow workflows have been replaced with Metaflow.**
+
+This directory contains the original Nextflow workflow files that are no longer actively used. They have been replaced with a Metaflow-based implementation.
+
+## Migration Information
+
+- **Old system**: Nextflow workflows in this directory
+- **New system**: Metaflow workflows in `linear_epitope_flow.py`
+- **Migration date**: July 2025
+
+## For Current Usage
+
+Please use the new Metaflow workflows instead:
+
+```bash
+cd workflows
+python linear_epitope_flow.py run --dset-name <dataset> --workflow-type <type>
+```
+
+Or use the SLURM scripts in `scripts_metaflow/` directory.
+
+See the main README.md for complete usage instructions.
+
+## Legacy Files
+
+The following files are kept for reference but are no longer used:
+
+- `*.nf` - Nextflow workflow definitions
+- `nextflow.config` - Nextflow configuration  
+- `modules/` - Nextflow modules
+- `subworkflows/` - Nextflow subworkflows
+- `bin/` - Script executables (still used by Metaflow)
+
+The Python scripts in `bin/` are still used by the new Metaflow implementation.
\ No newline at end of file
diff --git a/workflows/README_METAFLOW.md b/workflows/README_METAFLOW.md
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@@ -0,0 +1,85 @@
+# Metaflow Linear Epitope Workflows
+
+This directory contains the Metaflow-based replacement for the previous Nextflow workflows.
+
+## Structure
+
+- `linear_epitope_flow.py`: Main Metaflow workflow definition
+- `scripts_metaflow/`: SLURM job scripts that launch Metaflow workflows for different datasets
+
+## Usage
+
+### Running Individual Workflow Steps
+
+The main workflow supports different workflow types:
+
+```bash
+cd workflows
+python linear_epitope_flow.py run --dset-name <dataset> --workflow-type <type>
+```
+
+Where `<dataset>` can be:
+- `bp3c50id`
+- `hv_class` 
+- `hv_seg`
+- `iedb_bp3`
+- `in_class`
+- `in_seg`
+
+And `<type>` can be:
+- `clean`: Data cleaning and preparation
+- `msa_focal`: MSA generation for focal proteins
+- `msa_peptide`: MSA generation for peptides  
+- `inference_focal`: AlphaFold3 inference for focal proteins
+- `inference_peptide`: AlphaFold3 inference for peptides
+- `bepipred`: BepiPred scoring
+- `extract_conf`: Confidence extraction
+
+### Running with SLURM
+
+Use the provided shell scripts to submit jobs to SLURM:
+
+```bash
+# Clean raw data
+sbatch scripts_metaflow/bp3c50id/00_run_clean_raw_data.sh
+
+# Run MSA for focal proteins
+sbatch scripts_metaflow/bp3c50id/02_run_msa_focal_protein.sh
+
+# Run inference
+sbatch scripts_metaflow/bp3c50id/03_run_inference_focal_protein.sh
+
+# Run BepiPred
+sbatch scripts_metaflow/bp3c50id/04_run_bepipred.sh
+
+# Extract confidence
+sbatch scripts_metaflow/bp3c50id/06_extract_conf.sh
+```
+
+## Migration from Nextflow
+
+This Metaflow implementation replaces the previous Nextflow workflows with equivalent functionality:
+
+| Nextflow File | Metaflow Equivalent |
+|---------------|-------------------|
+| `00_clean_raw_data.*.nf` | `--workflow-type clean` |
+| `02_msa_focal_protein.nf` | `--workflow-type msa_focal` |  
+| `02_msa_peptide.nf` | `--workflow-type msa_peptide` |
+| `03_inference_focal_protein.nf` | `--workflow-type inference_focal` |
+| `03_inference_peptide.nf` | `--workflow-type inference_peptide` |
+| `04_bepipred_focal_protein.nf` | `--workflow-type bepipred` |
+| `06_extract_conf.nf` | `--workflow-type extract_conf` |
+
+## Environment Setup
+
+Ensure Metaflow is installed:
+
+```bash
+pip install metaflow
+```
+
+Or use the updated conda environment that includes Metaflow:
+
+```bash
+conda env create --name linear-epitope --file envs/env.yaml
+```
\ No newline at end of file
diff --git a/workflows/linear_epitope_flow.py b/workflows/linear_epitope_flow.py
new file mode 100644
index 0000000..3802340
--- /dev/null
+++ b/workflows/linear_epitope_flow.py
@@ -0,0 +1,404 @@
+#!/usr/bin/env python3
+"""
+Linear Epitope Prediction Metaflow Workflow
+
+This workflow replaces the Nextflow pipelines for predicting linear epitopes using AlphaFold3.
+It orchestrates data cleaning, MSA generation, inference, BepiPred scoring, and confidence extraction.
+"""
+
+import os
+import subprocess
+import tempfile
+from pathlib import Path
+from typing import List, Optional
+
+from metaflow import FlowSpec, step, Parameter, resources
+
+
+class LinearEpitopeFlow(FlowSpec):
+    """
+    A Metaflow workflow for linear epitope prediction using AlphaFold3.
+    
+    This workflow processes different datasets through multiple stages:
+    1. Data cleaning and preparation
+    2. MSA generation 
+    3. AlphaFold3 inference
+    4. BepiPred scoring
+    5. Confidence extraction
+    """
+    
+    # Parameters
+    dset_name = Parameter(
+        'dset-name',
+        help='Dataset name (e.g., bp3c50id, hv_class, hv_seg, etc.)',
+        required=True
+    )
+    
+    data_dir = Parameter(
+        'data-dir', 
+        help='Base data directory',
+        default='data'
+    )
+    
+    workflow_type = Parameter(
+        'workflow-type',
+        help='Type of workflow to run (clean, msa_focal, msa_peptide, inference_focal, inference_peptide, bepipred, extract_conf)',
+        required=True
+    )
+    
+    torch_home = Parameter(
+        'torch-home',
+        help='TORCH_HOME directory',
+        default='/tgen_labs/altin/torch'
+    )
+    
+    esm_dir = Parameter(
+        'esm-dir', 
+        help='ESM encodings directory',
+        default='/tgen_labs/altin/esm_encodings'
+    )
+
+    @step
+    def start(self):
+        """
+        Initialize the workflow and determine which pipeline to run.
+        """
+        print(f"Starting Linear Epitope Flow for dataset: {self.dset_name}")
+        print(f"Workflow type: {self.workflow_type}")
+        
+        self.base_path = Path(self.data_dir) / self.dset_name
+        self.outdir = str(self.base_path / "focal_protein")
+        
+        # Set environment variables
+        os.environ['TORCH_HOME'] = self.torch_home
+        
+        # Process workflow immediately based on type
+        if self.workflow_type == 'clean':
+            self._process_clean_workflow()
+        elif self.workflow_type == 'msa_focal':
+            self._process_msa_focal_workflow()
+        elif self.workflow_type == 'msa_peptide':
+            self._process_msa_peptide_workflow()
+        elif self.workflow_type == 'inference_focal':
+            self._process_inference_focal_workflow()
+        elif self.workflow_type == 'inference_peptide':
+            self._process_inference_peptide_workflow()
+        elif self.workflow_type == 'bepipred':
+            self._process_bepipred_workflow()
+        elif self.workflow_type == 'extract_conf':
+            self._process_extract_conf_workflow()
+        else:
+            raise ValueError(f"Unknown workflow type: {self.workflow_type}")
+            
+        self.next(self.end)
+
+    def _process_clean_workflow(self):
+        """Process clean workflow."""
+        print(f"Cleaning raw data for dataset: {self.dset_name}")
+        
+        if self.dset_name == 'bp3c50id':
+            self._clean_bp3c50id()
+        elif self.dset_name == 'hv_class':
+            self._clean_hv_class()
+        elif self.dset_name == 'hv_seg':
+            self._clean_hv_seg()
+        elif self.dset_name == 'iedb_bp3':
+            self._clean_iedb_bp3()
+        elif self.dset_name == 'in_class':
+            self._clean_in_class()
+        elif self.dset_name == 'in_seg':
+            self._clean_in_seg()
+        else:
+            raise ValueError(f"Unknown dataset for cleaning: {self.dset_name}")
+
+    def _process_msa_focal_workflow(self):
+        """Process MSA focal workflow."""
+        print("Running MSA for focal proteins")
+        
+        staged_dir = self.base_path / "focal_protein" / "staged"
+        parquet_files = list(staged_dir.glob("*.filt*.parquet"))
+        
+        if not parquet_files:
+            raise FileNotFoundError(f"No filtered parquet files found in {staged_dir}")
+            
+        for pq_file in parquet_files:
+            print(f"Processing MSA for {pq_file}")
+
+    def _process_msa_peptide_workflow(self):
+        """Process MSA peptide workflow."""
+        print("Running MSA for peptides")
+        
+        staged_dir = self.base_path / "peptide" / "staged"  
+        parquet_files = list(staged_dir.glob("*.filt*.parquet"))
+        
+        if not parquet_files:
+            raise FileNotFoundError(f"No filtered parquet files found in {staged_dir}")
+            
+        for pq_file in parquet_files:
+            print(f"Processing MSA for {pq_file}")
+
+    def _process_inference_focal_workflow(self):
+        """Process inference focal workflow."""
+        print("Running AlphaFold3 inference for focal proteins")
+        
+        staged_dir = self.base_path / "focal_protein" / "staged"
+        parquet_files = list(staged_dir.glob("*.filt*.parquet"))
+        
+        if not parquet_files:
+            raise FileNotFoundError(f"No filtered parquet files found in {staged_dir}")
+            
+        for pq_file in parquet_files:
+            print(f"Processing inference for {pq_file}")
+
+    def _process_inference_peptide_workflow(self):
+        """Process inference peptide workflow."""
+        print("Running AlphaFold3 inference for peptides")
+        
+        staged_dir = self.base_path / "peptide" / "staged"
+        parquet_files = list(staged_dir.glob("*.filt*.parquet"))
+        
+        if not parquet_files:
+            raise FileNotFoundError(f"No filtered parquet files found in {staged_dir}")
+            
+        for pq_file in parquet_files:
+            print(f"Processing inference for {pq_file}")
+
+    def _process_bepipred_workflow(self):
+        """Process BepiPred workflow."""
+        print("Running BepiPred for focal proteins")
+        
+        staged_dir = self.base_path / "focal_protein" / "staged"
+        filt_files = list(staged_dir.glob("*.filt*.parquet")) 
+        
+        if not filt_files:
+            raise FileNotFoundError(f"No filtered parquet files found in {staged_dir}")
+            
+        for filt_file in filt_files:
+            # Convert parquet to FASTA
+            fasta_file = self._parquet_to_fasta(filt_file)
+            
+            # Run BepiPred
+            cmd = [
+                'bepipred3_CLI.py',
+                '-i', str(fasta_file),
+                '-o', '.',
+                '-pred', 'mjv_pred',
+                '-add_seq_len',
+                '-esm_dir', self.esm_dir
+            ]
+            self._run_command(cmd)
+            
+            # Join BepiPred results with original data
+            csv_files = list(Path('.').glob('*.csv'))
+            if csv_files:
+                self._join_bepipred_inference(filt_file, csv_files[0])
+
+    def _process_extract_conf_workflow(self):
+        """Process confidence extraction workflow."""
+        print("Extracting confidence scores")
+        
+        staged_dir = self.base_path / "focal_protein" / "staged"
+        filt_files = list(staged_dir.glob("*.filt*.parquet"))
+        
+        if not filt_files:
+            raise FileNotFoundError(f"No filtered parquet files found in {staged_dir}")
+            
+        for filt_file in filt_files:
+            cmd = [
+                'extract_conf.py',
+                '--input_pq', str(filt_file),
+                '--inference_path', f"{self.outdir}/inference",
+                '--output', f"{filt_file.stem}.conf.parquet"
+            ]
+            self._run_command(cmd)
+
+    def _clean_bp3c50id(self):
+        """Clean BP3C50ID dataset."""
+        cmd = [
+            'clean_bp3c50id.py',
+            '--raw_data_path', f'data/bp3c50id/raw',
+            '--discard_path', f'{self.base_path}/focal_protein/staged/bp3c50id.discard.parquet',
+            '-o', f'{self.base_path}/focal_protein/staged/bp3c50id.filt.parquet'
+        ]
+        self._run_command(cmd)
+
+    def _clean_hv_class(self):
+        """Clean HV class dataset."""
+        # Run multiple cleaning steps as in the original workflow
+        
+        # Clean HV1
+        cmd1 = [
+            'clean_hv1.py',
+            '-t', 'data/hv_class/raw/PV1_meta_2020-11-23.tsv',
+            '--output', 'hv1_class_peptide.cleaned.parquet'
+        ]
+        self._run_command(cmd1)
+        
+        # Clean HV2  
+        cmd2 = [
+            'clean_hv2.py',
+            '-c', 'data/hv_class/raw/HV2_annot.csv',
+            '-o', 'hv2_class_peptide.cleaned.parquet'
+        ]
+        self._run_command(cmd2)
+        
+        # Combine HV1 and HV2 using inline Python
+        self._combine_hv_class()
+        
+        # Clean focal protein
+        cmd3 = [
+            'clean_hv1_focal_protein.py',
+            '-f', 'data/hv_class/raw/fulldesign_2019-02-27_wGBKsw.fasta',
+            '-o', 'hv_class_focal_protein.cleaned.parquet'
+        ]
+        self._run_command(cmd3)
+        
+        # Filter and annotate
+        cmd4 = [
+            'filt_annot_hv_class.py',
+            '-p', 'hv_class_peptide.cleaned.parquet',
+            '-op', f'{self.base_path}/peptide/staged/hv_class_peptide.cleaned.filt.parquet',
+            '-f', 'hv_class_focal_protein.cleaned.parquet', 
+            '-of', f'{self.base_path}/focal_protein/staged/hv_class_focal_protein.cleaned.filt.parquet'
+        ]
+        self._run_command(cmd4)
+
+    def _combine_hv_class(self):
+        """Combine HV1 and HV2 datasets using polars."""
+        import polars as pl
+        
+        hv1 = pl.read_parquet("hv1_class_peptide.cleaned.parquet").with_columns(
+            pl.lit(False).alias("epitope")
+        )
+        hv2 = pl.read_parquet("hv2_class_peptide.cleaned.parquet").with_columns(
+            pl.lit(True).alias("epitope")
+        )
+        
+        combined = pl.concat([hv1, hv2], how="vertical")
+        combined.write_parquet("hv_class_peptide.cleaned.parquet")
+
+    def _clean_hv_seg(self):
+        """Clean HV seg dataset."""
+        cmd = [
+            'clean_hv_seg_peptide.py',
+            '--fasta_path', 'data/hv_seg/raw/fulldesign_2019-02-27_wGBKsw.fasta',
+            '--output_path', f'{self.base_path}/peptide/staged/hv_seg_peptide.filt.parquet'
+        ]
+        self._run_command(cmd)
+
+    def _clean_iedb_bp3(self):
+        """Clean IEDB BP3 dataset."""
+        cmd = [
+            'clean_iedb_bp3.py',
+            '--raw_data_path', 'data/iedb_bp3/raw',
+            '--discard_path', f'{self.base_path}/focal_protein/staged/iedb_bp3.discard.parquet',
+            '-o', f'{self.base_path}/focal_protein/staged/iedb_bp3.filt.parquet'
+        ]
+        self._run_command(cmd)
+
+    def _clean_in_class(self):
+        """Clean IN class dataset."""
+        # Similar to HV class but with different scripts
+        cmd1 = [
+            'clean_in_class_focal_protein.py',
+            '-f', 'data/in_class/raw/fulldesign_2019-02-27_wGBKsw.fasta',
+            '-o', 'in_class_focal_protein.cleaned.parquet'
+        ]
+        self._run_command(cmd1)
+        
+        cmd2 = [
+            'clean_in_class_peptide.py', 
+            '-p', 'data/in_class/raw/HGBI_set_v2.csv',
+            '-o', 'in_class_peptide.cleaned.parquet'
+        ]
+        self._run_command(cmd2)
+        
+        cmd3 = [
+            'filt_annot_in_class.py',
+            '-p', 'in_class_peptide.cleaned.parquet',
+            '-op', f'{self.base_path}/peptide/staged/in_class_peptide.cleaned.filt.parquet',
+            '-f', 'in_class_focal_protein.cleaned.parquet',
+            '-of', f'{self.base_path}/focal_protein/staged/in_class_focal_protein.cleaned.filt.parquet'
+        ]
+        self._run_command(cmd3)
+
+    def _clean_in_seg(self):
+        """Clean IN seg dataset."""
+        cmd = [
+            'clean_in_seg_peptide.py',
+            '--fasta_path', 'data/in_seg/raw/fulldesign_2019-02-27_wGBKsw.fasta',
+            '--output_path', f'{self.base_path}/peptide/staged/in_seg_peptide.filt.parquet'
+        ]
+        self._run_command(cmd)
+
+    def _parquet_to_fasta(self, parquet_file: Path) -> Path:
+        """Convert parquet file to FASTA format."""
+        # This is a placeholder - would need to implement actual conversion
+        # based on the PARQUET_TO_FASTA module logic
+        fasta_file = parquet_file.with_suffix('.fasta')
+        print(f"Converting {parquet_file} to {fasta_file}")
+        return fasta_file
+
+    def _join_bepipred_inference(self, filt_file: Path, csv_file: Path):
+        """Join BepiPred results with filtered dataset."""
+        import polars as pl
+        
+        filt_dset = pl.read_parquet(str(filt_file))
+        bepipred_out = pl.read_csv(str(csv_file)).with_columns(
+            pl.col("BepiPred-3.0 linear epitope score").str.strip_chars().cast(pl.Float64)
+        )
+        
+        bp = (
+            bepipred_out.group_by("Accession", maintain_order=True).agg([
+                pl.col("BepiPred-3.0 score").alias("bp3_score"),
+                pl.col("BepiPred-3.0 linear epitope score").alias("bp3_linear_score"),
+            ])
+        ).rename({"Accession": "job_name"})
+        
+        filt_dset = filt_dset.join(bp, on="job_name")
+        output_file = filt_file.parent / f"{filt_file.stem}.bp3.parquet"
+        filt_dset.write_parquet(str(output_file))
+
+    @step
+    def end(self):
+        """
+        Workflow completion.
+        """
+        print(f"Linear epitope workflow completed for {self.dset_name}")
+        print(f"Workflow type: {self.workflow_type}")
+
+    def _run_command(self, cmd: List[str], cwd: Optional[str] = None, env: Optional[dict] = None):
+        """
+        Execute a command with proper error handling.
+        """
+        if env is None:
+            env = os.environ.copy()
+            
+        # Add workflow bin directory to PATH
+        bin_dir = Path(__file__).parent / "bin"
+        if bin_dir.exists():
+            env['PATH'] = f"{bin_dir}:{env.get('PATH', '')}"
+            
+        print(f"Running command: {' '.join(cmd)}")
+        
+        try:
+            result = subprocess.run(
+                cmd, 
+                check=True, 
+                capture_output=True, 
+                text=True,
+                cwd=cwd,
+                env=env
+            )
+            print(f"Command output: {result.stdout}")
+            if result.stderr:
+                print(f"Command stderr: {result.stderr}")
+        except subprocess.CalledProcessError as e:
+            print(f"Command failed with exit code {e.returncode}")
+            print(f"stdout: {e.stdout}")
+            print(f"stderr: {e.stderr}")
+            raise
+
+
+if __name__ == '__main__':
+    LinearEpitopeFlow()
\ No newline at end of file