auto commit -> added subject task data

.github/AF.yml

@@ -0,0 +1,57 @@
+name: Task1 QC
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  process_raw:
+    runs-on: self-hosted
+    steps:
+      - name: checkout code and return recently uploaded file in /data
+        uses: actions/checkout@v2
+        run: |
+          git pull origin main
+          #!/bin/bash
+          data=$(ls -t /data/*.txt | head -n 1)
+
+      - name: set up python
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+
+      - name: parse raw
+        run: |
+          // add bash to parse raw data filename, split by '_', and save as local variable
+          #!/bin/bash
+          filename=$(basename $data)
+          IFS='_' read -r sub task version <<< "$filename"
+          echo "sub=$sub" >> $GITHUB_ENV
+          echo "task=$task" >> $GITHUB_ENV
+          echo "version=$version" >> $GITHUB_ENV
+          echo "Subject: $sub"
+          echo "Task: $task"
+          echo "Version: $version"
+
+      - name: convert raw
+        run: python code/ConvertBeh.py -submission $data -out data/$sub/processed
+
+  run_qc:
+    runs-on: self-hosted
+    needs: process_raw
+    steps:
+      - name: run quality control
+        run: python AFqC.py -s data/$sub/processed/${sub}*.csv -o data/$sub/ -sub $sub | tee data/$sub/qc.log
+
+  push:
+    runs-on: self-hosted
+    needs: run_qc
+    steps:
+      - name: push results
+        run: |
+          git config user.email [email protected]
+          git config user.name "Zak Gilliam"
+          git remote set-url origin //insert PAT
+          git add -A
+          git commit -m "QC results for ${sub}"
+          git push origin main

.github/workflows/main.yml

@@ -22,16 +22,14 @@ jobs:
         run: |
           IFS='_' read -r sub task version <<< "$data"
           echo "sub=$sub" >> $GITHUB_ENV
-          echo "task=$task" >> $GITHUB_ENV
           echo "version=$version" >> $GITHUB_ENV
           echo "Subject: $sub"
-          echo "Task: $task"
           echo "Version: $version"
 
       - name: convert raw
         run: |
-          mkdir data/${sub}/processed
-          python code/ConvertBeh.py -submission $data -out data/$sub/processed -sub $sub -task $task -taskvers $version
+          mkdir data/${sub}/processed \
+          python code/ConvertBeh.py -submission $data -out data/$sub/processed -sub $sub -task AF -taskvers $version
 
   run_qc:
     runs-on: self-hosted