fix: fix workflow

Author: igboyes

Dockerfile

@@ -1,21 +1,19 @@
 FROM python:3.13-bookworm AS build
 WORKDIR /app
-RUN curl -sSL https://install.python-poetry.org | python -
-ENV PATH="/root/.local/bin:${PATH}" \
-    POETRY_CACHE_DIR='/tmp/poetry_cache' \
-    POETRY_NO_INTERACTION=1 \
-    POETRY_VIRTUALENVS_IN_PROJECT=1 \
-    POETRY_VIRTUALENVS_CREATE=1
-COPY pyproject.toml poetry.lock ./
-RUN poetry install --without dev --no-root
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+ENV UV_COMPILE_BYTECODE=1 \
+    UV_LINK_MODE=copy
+COPY pyproject.toml uv.lock ./
+RUN --mount=type=cache,target=/root/.cache/uv \
+    uv sync --locked --no-install-project --no-dev
 
 FROM python:3.13-bookworm AS base
 WORKDIR /app
 RUN apt-get update && \
     apt-get install -y --no-install-recommends default-jre && \
     rm -rf /var/lib/apt/lists/* && \
     apt-get clean
-COPY --from=ghcr.io/virtool/workflow-tools:2.0.1 /opt/fastqc /opt/fastqc
+COPY --from=ghcr.io/virtool/tools:1.1.0 /tools/fastqc/0.11.9/ /opt/fastqc
 ENV VIRTUAL_ENV=/app/.venv \
     PATH="/app/.venv/bin/:/opt/fastqc:${PATH}"
 RUN chmod ugo+x /opt/fastqc/fastqc

workflow.py

@@ -3,10 +3,10 @@
 from types import SimpleNamespace
 
 from pyfixtures import fixture
-from virtool_workflow import hooks, step
-from virtool_workflow.analysis.fastqc import FastQCRunner
-from virtool_workflow.analysis.utils import ReadPaths
-from virtool_workflow.data.samples import WFNewSample
+from virtool.quality.fastqc import parse_fastqc
+from virtool.workflow import hooks, step, RunSubprocess
+from virtool.workflow.analysis import ReadPaths
+from virtool.workflow.data.samples import WFNewSample
 
 
 @fixture
@@ -24,19 +24,30 @@ def read_paths(new_sample: WFNewSample) -> ReadPaths:
 
 @step(name="Run FastQC")
 async def run_fastqc(
-    fastqc: FastQCRunner,
     intermediate: SimpleNamespace,
     read_paths: ReadPaths,
+    run_subprocess: RunSubprocess,
     work_path: Path,
 ):
     """
     Run `fastqc` on the read files.
 
     Parse the output into a dictionary and add it to the scope.
     """
-    output_path = work_path / "fastqc"
-    await asyncio.to_thread(output_path.mkdir)
-    intermediate.quality = await fastqc(read_paths, output_path)
+    command = [
+        "fastqc",
+        "-f",
+        "fastq",
+        "-o",
+        str(work_path),
+        "--extract",
+        *[str(path) for path in read_paths],
+    ]
+
+    await run_subprocess(command)
+
+    intermediate.quality = await asyncio.to_thread(parse_fastqc, work_path)
+
 
 
 @step
@@ -51,9 +62,9 @@ async def finalize(
     """
     for i, path in enumerate(read_paths):
         new_path = await asyncio.to_thread(path.rename, f"reads_{i + 1}.fq.gz")
-        await new_sample.upload(new_path, "fastq")
+        await new_sample.upload(new_path)
 
-    await new_sample.finalize(intermediate.quality)
+    await new_sample.finalize(intermediate.quality.dict())
 
 
 @hooks.on_failure