fix: don't block ping while running subtraction elimination

Author: igboyes

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: ci
+name: CI
 
 on:
   pull_request:
@@ -24,6 +24,7 @@ jobs:
       - name: commitlint
         uses: wagoid/commitlint-github-action@v5
   build:
+    name: Build
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
@@ -39,6 +40,7 @@ jobs:
           cache-from: type=gha
           cache-to: type=gha,mode=max
   test:
+    name: Test
     runs-on: ubuntu-24.04
     steps:
       - name: Checkout
@@ -57,6 +59,7 @@ jobs:
       - name: Test
         run: docker run --rm -t ${{ steps.build.outputs.imageid }} poetry run pytest
   release:
+    name: "Publish / Release"
     runs-on: ubuntu-24.04
     if: github.event_name == 'push' || github.event_name == 'workflow_dispatch'
     needs: [build, commitlint, test]
@@ -77,6 +80,7 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: npx semantic-release
   ghcr:
+    name: "Publish / GHCR"
     runs-on: ubuntu-24.04
     if: |
       github.repository_owner == 'Virtool' &&

workflow.py

@@ -46,10 +46,13 @@ def subtract_fastq(
     new_fastq_path: Path,
     subtracted_reads: set[str],
 ):
-    with open(current_fastq_path) as current_fastq_file, open(
-        new_fastq_path,
-        "w",
-    ) as new_fastq_file:
+    with (
+        open(current_fastq_path) as current_fastq_file,
+        open(
+            new_fastq_path,
+            "w",
+        ) as new_fastq_file,
+    ):
         for record in read_fastq_grouped_lines(current_fastq_file):
             if record[0].strip("@\n") not in subtracted_reads:
                 new_fastq_file.write("".join(record))
@@ -284,7 +287,8 @@ async def eliminate_subtraction(
             ],
         )
 
-        run_eliminate_subtraction(
+        await asyncio.to_thread(
+            run_eliminate_subtraction,
             str(current_sam_input_path),
             str(to_subtraction_sam_path),
             str(subtracted_sam_path),