diff --git a/envs/Dockerfile b/envs/Dockerfile index 5e83cd2..5c9b2df 100644 --- 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 [] \ No newline at end of file +ENTRYPOINT [] diff --git a/envs/build-docker-imgs.sh b/envs/build-docker-imgs.sh index ebdc93c..9ec770c 100755 --- 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 index 4fef02a..525a33d 100644 --- 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 ) -} \ No newline at end of file +} diff --git a/multimodal.nf b/multimodal.nf index 26ac7c7..a67832a 100644 --- 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 index 5053afa..b5bb7e3 100644 --- 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 { } } -} \ No newline at end of file +} diff --git a/sphinx/conf.py b/sphinx/conf.py index 97dc463..f54fde9 100644 --- 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 index f377346..55e9018 100644 --- 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 \ No newline at end of file +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 index 5b6eddf..184ec37 100644 --- 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 \ No newline at end of file +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 index cea0c35..d129f21 100644 --- a/sphinx/installation.rst +++ b/sphinx/installation.rst @@ -17,7 +17,7 @@ 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 @@ -25,17 +25,17 @@ Using `wget` 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: