From 0c2d33d09701c82ec286f0f308dbf76074902a46 Mon Sep 17 00:00:00 2001 From: Arnaud Bore Date: Thu, 29 May 2025 15:42:19 -0400 Subject: [PATCH 1/2] Update Dockerfile Fix miniconda version. Due to some python package dependencies python 3.13 does not work yet. --- .devcontainer/Dockerfile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index d9d2e5d..2998c83 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -49,9 +49,9 @@ ENV NFCORE_SUBWORKFLOWS_BRANCH=main ENV PATH="/root/miniconda3/bin:${PATH}" RUN arch=$(uname -m) && \ if [ "$arch" = "x86_64" ]; then \ - MINICONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"; \ + MINICONDA_URL="https://repo.anaconda.com/miniconda//Miniconda3-py312_25.3.1-1-Linux-x86_64.sh"; \ elif [ "$arch" = "aarch64" ]; then \ - MINICONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh"; \ + MINICONDA_URL="https://repo.anaconda.com/miniconda/Miniconda3-py312_25.3.1-1-Linux-aarch64.sh"; \ else \ echo "Unsupported architecture: $arch"; \ exit 1; \ From a39c056e01edb70915365d54b3841f3ea5da1a95 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Fri, 7 Nov 2025 13:28:12 -0500 Subject: [PATCH 2/2] update path to new organization --- .devcontainer/Dockerfile | 6 +++--- modules.json | 2 +- nextflow.config | 2 +- nf-test.config | 2 +- tests/plugins.json | 6 +++--- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 2998c83..cfb88b2 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -39,10 +39,10 @@ ENV NXF_EDGE=0 ENV NXF_VER=24.10.4 ENV NXF_HOME=/workspaces/.nextflow -ENV NFNEURO_RAW_REPOSITORY="https://raw.githubusercontent.com/scilus/nf-neuro/main" -ENV NFCORE_MODULES_GIT_REMOTE=https://github.com/scilus/nf-neuro.git +ENV NFNEURO_RAW_REPOSITORY="https://raw.githubusercontent.com/nf-neuro/modules/main" +ENV NFCORE_MODULES_GIT_REMOTE=https://github.com/nf-neuro/modules.git ENV NFCORE_MODULES_BRANCH=main -ENV NFCORE_SUBWORKFLOWS_GIT_REMOTE=https://github.com/scilus/nf-neuro.git +ENV NFCORE_SUBWORKFLOWS_GIT_REMOTE=https://github.com/nf-neuro/modules.git ENV NFCORE_SUBWORKFLOWS_BRANCH=main # Install conda diff --git a/modules.json b/modules.json index 7dd2540..d303a20 100644 --- a/modules.json +++ b/modules.json @@ -2,7 +2,7 @@ "name": "", "homePage": "", "repos": { - "https://github.com/scilus/nf-neuro.git": { + "https://github.com/nf-neuro/modules.git": { "modules": { "nf-neuro": { "reconst/dtimetrics": { diff --git a/nextflow.config b/nextflow.config index a04f14f..853b11f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -12,7 +12,7 @@ profiles { } manifest { - name = 'scilus/nf-neuro-tutorial' + name = 'nf-neuro/tutorial' description = """nf-neuro-tutorial is a Nextflow pipeline for processing neuroimaging data.""" version = '0.1dev' } diff --git a/nf-test.config b/nf-test.config index 12db2c1..e9eb688 100644 --- a/nf-test.config +++ b/nf-test.config @@ -11,7 +11,7 @@ config { ignore ".venv/**/*.nf*" plugins { - repository "https://raw.githubusercontent.com/scilus/nf-neuro/main/tests/plugins.json" + repository "https://raw.githubusercontent.com/nf-neuro/modules/main/tests/plugins.json" load "nft-nifti@0.0.1" } diff --git a/tests/plugins.json b/tests/plugins.json index 08631db..318a518 100644 --- a/tests/plugins.json +++ b/tests/plugins.json @@ -2,15 +2,15 @@ { "id": "nft-nifti", "latest": "0.0.1", - "url": "https://github.com/scilus/nft-nifti", - "github": "scilus/nft-nifti", + "url": "https://github.com/nf-neuro/nft-nifti", + "github": "nf-neuro/nft-nifti", "description": "Provides support for NIFTI files.", "author": "Arnaud Boré and Alex V Caron", "keywords": [], "releases": [ { "version": "0.0.1", - "url": "https://github.com/scilus/nft-nifti/releases/download/0.0.1/nft-nifti-0.0.1.jar" + "url": "https://github.com/nf-neuro/nft-nifti/releases/download/0.0.1/nft-nifti-0.0.1.jar" } ] }