Fixed bioformats2raw version across environments (#149)

StasMakarchuk · web-flow · commit a9b9d5d42a01 · 2024-12-02T13:13:28.000Z
* Update nextflow.config
* Update Dockerfile
* Update build-docker-imgs.sh
* Update main.nf
* Update multimodal.nf
* Update conf.py
* Update visium.rst
* Update xenium.rst
* Update installation.rst
diff --git a/envs/Dockerfile b/envs/Dockerfile
@@ -1,5 +1,5 @@
 FROM python:3.10
-ARG BIOFORMATS2RAW="0.4.0"
+ARG BIOFORMATS2RAW="0.7.0"
 
 COPY ./requirements.txt /requirements.txt
 RUN apt-get update && \
@@ -15,4 +15,4 @@ RUN apt-get update && \
 RUN pip install --upgrade pip setuptools distlib --no-cache-dir && \
     pip install --no-cache-dir -r /requirements.txt
 
-ENTRYPOINT []
+ENTRYPOINT []
diff --git a/envs/build-docker-imgs.sh b/envs/build-docker-imgs.sh
@@ -1,5 +1,5 @@
 #! /bin/sh
-VERSION=0.5.2
+VERSION=0.5.3
 
 #
 # Build local docker images
diff --git a/main.nf b/main.nf
@@ -5,7 +5,7 @@ import groovy.json.*
 nextflow.enable.dsl=2
 
 verbose_log = true
-version = "0.5.2"
+version = "0.5.3"
 
 //////////////////////////////////////////////////////
 
@@ -480,4 +480,4 @@ workflow Output_to_spatialdata {
             data_for_sd
         )
         
-}
+}
diff --git a/multimodal.nf b/multimodal.nf
@@ -11,7 +11,7 @@ params.outdir = ""
 params.copy_raw = true
 params.description = ""
 
-version="0.5.2"
+version="0.5.3"
 verbose_log=true
 outdir_with_version = "${params.outdir.replaceFirst(/\/*$/, "")}\/${version}"
 
diff --git a/nextflow.config b/nextflow.config
@@ -13,7 +13,7 @@ profiles {
   docker { 
     docker.enabled = true
     process {
-      container = 'haniffalab/webatlas-pipeline:0.5.2'
+      container = 'haniffalab/webatlas-pipeline:0.5.3'
       withLabel: build_config {
         container = 'haniffalab/webatlas-pipeline-build-config:0.5.2'
       }
@@ -31,4 +31,4 @@ profiles {
     }
   }
 
-}
+}
diff --git a/sphinx/conf.py b/sphinx/conf.py
@@ -23,7 +23,7 @@
 author = "Haniffa Lab"
 
 # The full version, including alpha/beta/rc tags
-release = "0.5.2"
+release = "0.5.3"
 
 # -- General configuration ---------------------------------------------------
 
diff --git a/sphinx/examples/visium.rst b/sphinx/examples/visium.rst
@@ -150,7 +150,7 @@ verify the expected directories are created.
 .. code-block:: shell
    :caption: Input
 
-   ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.5.2
+   ls -l output/CytAssist_FFPE_Human_Breast_Cancer/0.5.3
 
 .. code-block:: shell
    :caption: Output
@@ -174,7 +174,7 @@ at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-
 .. code-block:: shell
    :caption: Input
 
-   npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.5.2 --port 3000 --cors
+   npx http-server output/CytAssist_FFPE_Human_Breast_Cancer/0.5.3 --port 3000 --cors
 
 .. code-block:: shell
    :caption: Output
@@ -204,4 +204,4 @@ at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-
 
 Start your web browser and open:
 
-https://webatlas.cog.sanger.ac.uk/latest/index.html?theme=dark&config=http://127.0.0.1:3000/visium-breast-cancer-config.json
+https://webatlas.cog.sanger.ac.uk/latest/index.html?theme=dark&config=http://127.0.0.1:3000/visium-breast-cancer-config.json
diff --git a/sphinx/examples/xenium.rst b/sphinx/examples/xenium.rst
@@ -141,7 +141,7 @@ verify the expected directories are created.
 .. code-block:: shell
    :caption: Input
 
-   ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.5.2
+   ls -l output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.5.3
 
 .. code-block:: shell
    :caption: Output
@@ -164,7 +164,7 @@ at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-
 .. code-block:: shell
    :caption: Input
 
-   npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.5.2 --port 3000 --cors
+   npx http-server output/Xenium_FFPE_Human_Breast_Cancer_Rep1_outs/0.5.3 --port 3000 --cors
 
 .. code-block:: shell
    :caption: Output
@@ -194,4 +194,4 @@ at http://localhost:3000, and that CORS is enabled via the Access-Control-Allow-
 
 Start your web browser and open:
 
-https://webatlas.cog.sanger.ac.uk/latest/index.html?theme=dark&config=http://127.0.0.1:3000/xenium-breast-cancer-config.json
+https://webatlas.cog.sanger.ac.uk/latest/index.html?theme=dark&config=http://127.0.0.1:3000/xenium-breast-cancer-config.json
diff --git a/sphinx/installation.rst b/sphinx/installation.rst
@@ -17,25 +17,25 @@ Using `wget`
 .. code-block:: shell
    :caption: Input
 
-   wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.2.tar.gz
+   wget https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.3.tar.gz
 
 .. code-block:: shell
    :caption: Expected Output
 
    Resolving github.com (github.com)... 140.82.121.3
    Connecting to github.com (github.com)|140.82.121.3|:443... connected.
    HTTP request sent, awaiting response... 302 Found
-   Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.2 [following]
-   --2023-05-18 09:30:15--  https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.2
+   Location: https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.3 [following]
+   --2023-05-18 09:30:15--  https://codeload.github.com/haniffalab/webatlas-pipeline/tar.gz/refs/tags/v0.5.3
    Resolving codeload.github.com (codeload.github.com)... 140.82.121.9
    Connecting to codeload.github.com (codeload.github.com)|140.82.121.9|:443... connected.
    HTTP request sent, awaiting response... 200 OK
    Length: unspecified [application/x-gzip]
-   Saving to: ‘v0.5.2.tar.gz’
+   Saving to: ‘v0.5.3.tar.gz’
 
-   v0.5.2.tar.gz [ <=>                                           ]   2.70M  9.12MB/s    in 0.3s    
+   v0.5.3.tar.gz [ <=>                                           ]   2.70M  9.12MB/s    in 0.3s    
 
-   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.2.tar.gz’ saved [2835534]
+   2023-05-18 09:30:16 (9.12 MB/s) - ‘v0.5.3.tar.gz’ saved [2835534]
 
 
 Using `curl`
@@ -44,7 +44,7 @@ Using `curl`
 .. code-block:: shell
    :caption: Input
 
-   curl -L -o v0.5.2.tar.gz https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.2.tar.gz
+   curl -L -o v0.5.3.tar.gz https://github.com/haniffalab/webatlas-pipeline/archive/refs/tags/v0.5.3.tar.gz
 
 .. code-block:: shell
    :caption: Expected Output
@@ -60,18 +60,18 @@ Extract the WebAtlas compressed tag and change directory into the new repo.
 .. code-block:: shell
    :caption: Input
 
-   tar -xzvf ./v0.5.2.tar.gz
-   cd webatlas-pipeline-0.5.2
+   tar -xzvf ./v0.5.3.tar.gz
+   cd webatlas-pipeline-0.5.3
 
 .. code-block:: shell
    :caption: Expected Output
     
-   webatlas-pipeline-0.5.2/
-   webatlas-pipeline-0.5.2/.github/
+   webatlas-pipeline-0.5.3/
+   webatlas-pipeline-0.5.3/.github/
    ...
    ...
-   webatlas-pipeline-0.5.2/tests/input/simple_config.json
-   webatlas-pipeline-0.5.2/tests/test_class.py
+   webatlas-pipeline-0.5.3/tests/input/simple_config.json
+   webatlas-pipeline-0.5.3/tests/test_class.py
 
 .. _environment:
 

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,5 @@`
`1`	`1`	`#! /bin/sh`
`2`		`-VERSION=0.5.2`
	`2`	`+VERSION=0.5.3`
`3`	`3`
`4`	`4`	`#`
`5`	`5`	`# Build local docker images`
Original file line number	Diff line number	Diff line change
`@@ -13,7 +13,7 @@ profiles {`
`13`	`13`	`docker {`
`14`	`14`	`docker.enabled = true`
`15`	`15`	`process {`
`16`		`- container = 'haniffalab/webatlas-pipeline:0.5.2'`
	`16`	`+ container = 'haniffalab/webatlas-pipeline:0.5.3'`
`17`	`17`	`withLabel: build_config {`
`18`	`18`	`container = 'haniffalab/webatlas-pipeline-build-config:0.5.2'`
`19`	`19`	`}`
`@@ -31,4 +31,4 @@ profiles {`
`31`	`31`	`}`
`32`	`32`	`}`
`33`	`33`
`34`		`-}`
	`34`	`+}`