feat: add accbase target for ATAC-seq/DNase-seq discovery

Add support for discovering chromatin accessibility datasets (ATAC-seq,
scATAC-seq, DNase-seq) from GEO and uploading them to the accbase
namespace in PEPhub.

- Add "accbase" to valid targets in CLI
- Add ACCBASE_FINDER_FILTER and ACCBASE_MAX_SIZE constants
- Add accbase branches in queuer (assay-type filter) and uploader
- Add accbase_uploader.yml and accbase_checker.yml GitHub Actions
- Update README with accbase documentation

Author: nsheff

.github/workflows/accbase_checker.yml

@@ -0,0 +1,35 @@
+name: Check failed cycles and samples for accbase
+
+on:
+  schedule:
+    # run every 2 days at 13:00 (offset from bedbase)
+    - cron: '0 13 1/2 * *'
+  workflow_dispatch:
+
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    env:
+      POSTGRES_DB: ${{ secrets.POSTGRES_DB }}
+      POSTGRES_HOST: ${{ secrets.POSTGRES_HOST }}
+      POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
+      POSTGRES_PORT: ${{ secrets.POSTGRES_PORT }}
+      POSTGRES_USER: ${{ secrets.POSTGRES_USER }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      - name: Install package
+        run: python -m pip install .
+
+      - name: Check cycles 1-5
+        run: |
+          for cycle in 1 2 3 4 5; do
+            echo "Checking cycle $cycle..."
+            geopephub run-checker --target accbase --period 2 --cycle-count $cycle
+          done

.github/workflows/accbase_uploader.yml

@@ -0,0 +1,34 @@
+name: Queue and upload Accbase projects
+
+on:
+  schedule:
+    # run every 2 days at 12:00 (offset from bedbase)
+    - cron: '0 12 1/2 * *'
+  workflow_dispatch:
+
+jobs:
+  upload:
+    runs-on: ubuntu-latest
+    env:
+      POSTGRES_DB: ${{ secrets.POSTGRES_DB }}
+      POSTGRES_HOST: ${{ secrets.POSTGRES_HOST }}
+      POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
+      POSTGRES_PORT: ${{ secrets.POSTGRES_PORT }}
+      POSTGRES_USER: ${{ secrets.POSTGRES_USER }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Set up Python
+        uses: actions/setup-python@v6
+        with:
+          python-version: '3.12'
+
+      - name: Install package
+        run: python -m pip install .
+
+      - name: Add to queue
+        run: geopephub run-queuer --target accbase --period 2
+
+      - name: Upload to PEPhub
+        run: geopephub run-uploader --target accbase

README.md

@@ -4,6 +4,14 @@
 This repository contains `geopephub` CLI, that enables to automatic upload GEO projects to PEPhub based on date and scheduled automatic uploading using GitHub actions. 
 Additionally, the CLI includes a download command, enabling users to retrieve projects from specified namespace directly from the PEPhub database. This feature is particularly helpful for downloading all GEO projects at once.
 
+## Supported Targets
+
+The pipeline supports three targets:
+
+- **geo**: All GEO projects (default behavior, no filtering)
+- **bedbase**: BED file projects - filters GEO for BED, narrowPeak, and broadPeak files, uploads to the `bedbase` namespace
+- **accbase**: Chromatin accessibility projects - filters GEO for ATAC-seq, scATAC-seq, and DNase-seq assays, uploads to the `accbase` namespace
+
 ## Installation
 To install `geopephub` use this command: 
 ```

geopephub/cli.py

@@ -15,10 +15,10 @@
 
 
 def validate_target(value: str):
-    valid_target = ["geo", "bedbase"]
+    valid_target = ["geo", "bedbase", "accbase"]
     if value.lower() not in valid_target:
         raise typer.BadParameter(
-            f"Invalid color '{value}'. Choose from: {', '.join(valid_target)}"
+            f"Invalid target '{value}'. Choose from: {', '.join(valid_target)}"
         )
     return value.lower()
 

geopephub/const.py

@@ -24,3 +24,7 @@
 POSTGRES_DIALECT = "postgresql+psycopg"
 
 BEDBASE_MAX_SIZE = "500MB"
+
+# Accbase specific constants
+ACCBASE_FINDER_FILTER = "((ATAC-seq) OR (scATAC-seq) OR (DNase-seq))"
+ACCBASE_MAX_SIZE = "1GB"

geopephub/metageo_pephub.py

@@ -11,7 +11,7 @@
 
 import peppy
 
-from geopephub.const import LAST_UPDATE_DATES, BEDBASE_MAX_SIZE
+from geopephub.const import LAST_UPDATE_DATES, BEDBASE_MAX_SIZE, ACCBASE_FINDER_FILTER, ACCBASE_MAX_SIZE
 from geopephub.utils import get_agent, get_base_db_engine
 from geopephub.models import StatusModel, CycleModel
 from geopephub.utils import run_geofetch, add_link_to_description
@@ -59,6 +59,11 @@ def add_to_queue_by_period(
         gse_list = geofetch.Finder(
             filters="((bed) OR narrowPeak) OR broadPeak"
         ).get_gse_by_date(start_date_str, today_date_str)
+    elif target == "accbase":
+        # get chromatin accessibility projects (ATAC-seq, scATAC-seq, DNase-seq)
+        gse_list = geofetch.Finder(
+            filters=ACCBASE_FINDER_FILTER
+        ).get_gse_by_date(start_date_str, today_date_str)
     elif target == "geo":
         gse_list = geofetch.Finder().get_gse_by_date(start_date_str, today_date_str)
     else:
@@ -195,6 +200,14 @@ def _upload_gse_project(
             data_source="all",
             processed=True,
         )
+    elif target == "accbase":
+        # For accbase, we want all files from ATAC-seq/DNase-seq projects
+        # No file extension filter - we filter by assay type in the Finder
+        geofetcher_obj = geofetch.Geofetcher(
+            filter_size=ACCBASE_MAX_SIZE,
+            data_source="all",
+            processed=True,
+        )
     else:
         geofetcher_obj = geofetch.Geofetcher()
     total_nb = len(log_model_dict.keys())
@@ -254,6 +267,8 @@ def _upload_gse_project(
             gse_log.status_info = "pepdbagent"
             if target == "bedbase":
                 tag = pep_tag
+            elif target == "accbase":
+                tag = pep_tag
             else:
                 tag = "default"
             try: