feat(qc): add Dockerfiles to build the QC containers from environment.yml

Each module's Dockerfile builds its container (micromamba base + the pinned
environment.yml, Quarto env vars set) so the images are reproducible and ready
to be rebuilt / migrated to the nf-core org.

Co-authored-by: Malwina Prater <mprater@altoslabs.com>
Co-authored-by: Nell Nie <nnie@altoslabs.com>
Co-authored-by: Christel Krueger <ckrueger@altoslabs.com>

Author: 4 people

modules/local/image_qc/Dockerfile

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+# Container for the image QC module (analysis + Quarto report).
+# Built from environment.yml in this directory. Tagged and pushed as
+# quay.io/dongzehe/image_qc:1.0.0 (to be migrated to the nf-core org for release).
+#
+#   docker build -t quay.io/<namespace>/image_qc:1.0.0 modules/local/image_qc
+#
+# Note: behind a corporate proxy / private conda mirror you may need to provide a
+# CA bundle and channel config at build time (e.g. via BuildKit --mount=type=secret);
+# a standard build resolves the pinned packages directly from conda-forge/bioconda.
+FROM mambaorg/micromamba:2.0.5
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+RUN micromamba install -y -n base -f /tmp/environment.yml \
+    && micromamba clean -a -f -y \
+    && rm -f /tmp/environment.yml
+ENV PATH="/opt/conda/bin:$PATH" \
+    QUARTO_DENO=/opt/conda/bin/deno \
+    QUARTO_DENO_DOM=/opt/conda/lib/deno_dom.so \
+    QUARTO_PANDOC=/opt/conda/bin/pandoc \
+    QUARTO_ESBUILD=/opt/conda/bin/esbuild \
+    QUARTO_TYPST=/opt/conda/bin/typst \
+    QUARTO_DART_SASS=/opt/conda/bin/sass \
+    QUARTO_SHARE_PATH=/opt/conda/share/quarto \
+    QUARTO_CONDA_PREFIX=/opt/conda

modules/local/transcript_qc/Dockerfile

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+# Container for the transcript QC module (analysis + Quarto report).
+# Built from environment.yml in this directory. Tagged and pushed as
+# quay.io/dongzehe/transcript_qc:1.0.0 (to be migrated to the nf-core org for release).
+#
+#   docker build -t quay.io/<namespace>/transcript_qc:1.0.0 modules/local/transcript_qc
+#
+# Note: behind a corporate proxy / private conda mirror you may need to provide a
+# CA bundle and channel config at build time (e.g. via BuildKit --mount=type=secret);
+# a standard build resolves the pinned packages directly from conda-forge/bioconda.
+FROM mambaorg/micromamba:2.0.5
+COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
+RUN micromamba install -y -n base -f /tmp/environment.yml \
+    && micromamba clean -a -f -y \
+    && rm -f /tmp/environment.yml
+ENV PATH="/opt/conda/bin:$PATH" \
+    QUARTO_DENO=/opt/conda/bin/deno \
+    QUARTO_DENO_DOM=/opt/conda/lib/deno_dom.so \
+    QUARTO_PANDOC=/opt/conda/bin/pandoc \
+    QUARTO_ESBUILD=/opt/conda/bin/esbuild \
+    QUARTO_TYPST=/opt/conda/bin/typst \
+    QUARTO_DART_SASS=/opt/conda/bin/sass \
+    QUARTO_SHARE_PATH=/opt/conda/share/quarto \
+    QUARTO_CONDA_PREFIX=/opt/conda