cellpheno/nis: align version to 1.0.2; fix README

Container tag, versions-topic string and Dockerfile VERSION were still 1.0.0
while the pinned source and bioconda package are 1.0.2 -> align all to 1.0.2.
Fix README (binary is installed as cellpheno-nis, not main; accurate release
steps). Regenerate stub snapshot.

Author: Chrisa142857

modules/nf-core/cellpheno/nis/Dockerfile

@@ -72,7 +72,7 @@ COPY --from=build /src/cpp/build/main /usr/local/bin/cellpheno-nis
 
 # Single authoritative version source. The module reads the NIS version from this file into versions.yml, so the container tag and the
 # reported version stay in lockstep. Bump together with the `container` tag in main.nf.
-ARG CELLPHENO_NIS_VERSION=1.0.0
+ARG CELLPHENO_NIS_VERSION=1.0.2
 RUN mkdir -p /usr/local/share/cellpheno-nis \
     && echo "${CELLPHENO_NIS_VERSION}" > /usr/local/share/cellpheno-nis/VERSION
 
@@ -83,7 +83,7 @@ LABEL org.opencontainers.image.authors="Ziquan Wei (@Chrisa142857)" \
       org.opencontainers.image.description="Whole-brain 3D nuclei instance segmentation for lightsheet microscopy" \
       org.opencontainers.image.source="https://github.com/Chrisa142857/Lightsheet_microscopy_image_3D_nuclei_instance_segmentation" \
       org.opencontainers.image.licenses="MIT" \
-      org.opencontainers.image.version="1.0.0"
+      org.opencontainers.image.version="1.0.2"
 
 ENTRYPOINT []
 CMD ["cellpheno-nis", "--help"]

modules/nf-core/cellpheno/nis/README.md

@@ -1,20 +1,31 @@
 # Updating the docker container and making a new module release
 
 The CellPheno NIS container is built from the [`Dockerfile`](./Dockerfile) in this
-directory. It clones the source repository and compiles the C++/LibTorch/CUDA executable,
-then ships it on `PATH` as `main`.
+directory. It clones a pinned release of the source repository, compiles the
+C++/LibTorch/CUDA executable, and installs it on `PATH` as `cellpheno-nis`.
 
 To update this tool:
 
-1. Edit the version (and, for a fixed build, the pinned source ref) in the `Dockerfile`:
+1. In the [`Dockerfile`](./Dockerfile), pin the source to the new release tag and bump the
+   reported version:
 
    ```diff
-   - ARG CELLPHENO_NIS_VERSION=1.0.0
+   - ARG NIS_SOURCE_REF=v1.0.2
+   + ARG NIS_SOURCE_REF=<new release tag>
+   - ARG CELLPHENO_NIS_VERSION=1.0.2
    + ARG CELLPHENO_NIS_VERSION=<new version>
    ```
 
-   and bump the `container` tag in [`main.nf`](./main.nf) to match.
+2. In [`main.nf`](./main.nf), bump the `container` tag and the version string in the
+   `versions` topic to match:
 
-2. Open a PR against [nf-core/modules](https://github.com/nf-core/modules), push the
-   changes, and the `Dockerfile` will be built and uploaded to
-   `quay.io/nf-core/cellpheno-nis`.
+   ```diff
+   - container "quay.io/nf-core/cellpheno-nis:1.0.2"
+   + container "quay.io/nf-core/cellpheno-nis:<new version>"
+   ...
+   - tuple val("${task.process}"), val('cellpheno-nis'), val('1.0.2'), topic: versions, ...
+   + tuple val("${task.process}"), val('cellpheno-nis'), val('<new version>'), topic: versions, ...
+   ```
+
+3. Open a PR against [nf-core/modules](https://github.com/nf-core/modules) and push the
+   changes; the `Dockerfile` is built and uploaded to `quay.io/nf-core/cellpheno-nis`.

modules/nf-core/cellpheno/nis/main.nf

@@ -8,7 +8,7 @@ process CELLPHENO_NIS {
     // It has no Conda/Bioconda package and requires a CUDA runtime, so it is
     // distributed only as a dedicated GPU container image (cf. the parabricks and
     // numorph/3dunet modules, which likewise ship a vendor GPU image with no conda).
-    container "quay.io/nf-core/cellpheno-nis:1.0.0"
+    container "quay.io/nf-core/cellpheno-nis:1.0.2"
 
     input:
     tuple val(meta), path(tile_dir)
@@ -17,7 +17,7 @@ process CELLPHENO_NIS {
     output:
     tuple val(meta), path("*_NIScpp_results_*.zip"), emit: nis
     tuple val(meta), path("*_remap.zip")           , emit: remap, optional: true
-    tuple val("${task.process}"), val('cellpheno-nis'), val('1.0.0'), topic: versions, emit: versions_cellpheno_nis // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    tuple val("${task.process}"), val('cellpheno-nis'), val('1.0.2'), topic: versions, emit: versions_cellpheno_nis // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     when:
     task.ext.when == null || task.ext.when

modules/nf-core/cellpheno/nis/meta.yml

@@ -74,7 +74,7 @@ output:
       - "cellpheno-nis":
           type: string
           description: The name of the tool
-      - "1.0.0":
+      - "1.0.2":
           type: string
           description: The expression to obtain the version of the tool
 topics:
@@ -85,7 +85,7 @@ topics:
       - "cellpheno-nis":
           type: string
           description: The name of the tool
-      - "1.0.0":
+      - "1.0.2":
           type: string
           description: The expression to obtain the version of the tool
 authors:

modules/nf-core/cellpheno/nis/tests/main.nf.test.snap

@@ -29,7 +29,7 @@
                     [
                         "CELLPHENO_NIS",
                         "cellpheno-nis",
-                        "1.0.0"
+                        "1.0.2"
                     ]
                 ],
                 "nis": [
@@ -59,7 +59,7 @@
                     [
                         "CELLPHENO_NIS",
                         "cellpheno-nis",
-                        "1.0.0"
+                        "1.0.2"
                     ]
                 ]
             }