Merge pull request #60 from DongzeHE/develop

feat: add toy run in github actions

.github/workflows/rust.yml

@@ -65,6 +65,40 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
 
+  sample_run:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+    - uses: actions/checkout@v2.4.2
+    - name: Install
+      run: cargo build --release
+    - name: sample run
+      run: |
+        wget https://umd.box.com/shared/static/75a80udhx51fjndbgnm6dmm25qsia5ks.gz -O toy_set.tar.gz
+        tar xzf toy_set.tar.gz
+        fry="target/release/alevin-fry"
+        threads=2
+        map_dir="toy_set/alevin_map"
+        gpl_dir="gpl"
+        quant_dir="quant"
+        permitmode="-u toy_set/10x_v3_permit.txt"
+        t2g="toy_set/t2g_3col.tsv"
+        res="cr-like"
+        ### generate permit list
+        cmd="$fry generate-permit-list $permitmode -d fw -i $map_dir -o $gpl_dir"
+        eval $cmd
+
+        ### collate
+        cmd="$fry collate -i $gpl_dir -r $map_dir -t $threads"
+        eval $cmd
+
+        ### quant
+        cmd="$fry quant -r $res --use-mtx -m $t2g -i $gpl_dir -o $quant_dir -t $threads"
+        eval $cmd
+
   # Coverage:
   #   if: "!contains(github.event.head_commit.message, 'skip ci')"
   #   needs: Formatting