From 960f202ad387c87bf6494a53eb0ee11c671cd86e Mon Sep 17 00:00:00 2001 From: Matthias Zepper Date: Mon, 23 Sep 2024 20:24:10 +0200 Subject: [PATCH] Fix GitHub Action in pipeline-template and update Changelog. --- CHANGELOG.md | 11 +++++++++++ nf_core/__main__.py | 2 +- .../.github/workflows/download_pipeline.yml | 2 +- 3 files changed, 13 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 30bd00b5c..b3777c8ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -69,6 +69,17 @@ - Components: allow spaces at the beginning of include statements ([#3115](https://github.com/nf-core/tools/pull/3115)) - Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077)) +### Download + +- Fully removed already deprecated `-t` / `--tower` flag. +- Refactored the CLI for consistency (short flag is usually second word, e.g. also for `--container-library` etc.): + +| Old parameter | New parameter | +| --------------------------------- | --------------------------------- | +| `-d` / `--download-configuration` | `-c` / `--download-configuration` | +| `-p` / `--parallel-downloads` | `-d` / `--parallel-downloads` | +| new parameter | `-p` / (`--platform`) | + ### General - Update output of generation script for API docs to new structure ([#2988](https://github.com/nf-core/tools/pull/2988)) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 98673fe1e..e0c1b85e9 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -412,7 +412,7 @@ def command_pipelines_lint( help="List of images already available in a remote `singularity.cacheDir`.", ) @click.option( - "-n", + "-d", "--parallel-downloads", type=int, default=4, diff --git a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml index e7a28e5ac..f704609ca 100644 --- a/nf_core/pipeline-template/.github/workflows/download_pipeline.yml +++ b/nf_core/pipeline-template/.github/workflows/download_pipeline.yml @@ -65,7 +65,7 @@ jobs: --container-system 'singularity' \ --container-library "quay.io" -l "docker.io" -l "ghcr.io" \ --container-cache-utilisation 'amend' \ - --download-configuration + --download-configuration 'yes' - name: Inspect download run: tree ./${{ env.REPOTITLE_LOWERCASE }}{% endraw %}{% if test_config %}{% raw %}