From f5a03700462f159095043eda19f6f8fa938d2987 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 11 Oct 2024 09:53:22 +0200 Subject: [PATCH 1/4] chore: checkout full history for formatting --- .github/workflows/main.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 51391772..fe93b6a9 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -23,6 +23,8 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 + with: + depth: 0 - name: Formatting uses: super-linter/super-linter@v5.7.2 env: From 05049d2223685a352a01b95a4da52895613bca5e Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Mon, 14 Oct 2024 16:04:56 +0200 Subject: [PATCH 2/4] force latest pangolin --- workflow/envs/pangolin.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml index f6a26ad4..3a8c7f9b 100644 --- a/workflow/envs/pangolin.yaml +++ b/workflow/envs/pangolin.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - pangolin =4.3 + - pangolin =4.3.1 From 18ebe5d73909a8a15212693131400bc059cbda56 Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Mon, 14 Oct 2024 16:29:20 +0200 Subject: [PATCH 3/4] work around pangolin dependency issues --- workflow/envs/pangolin.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml index 3a8c7f9b..42265aca 100644 --- a/workflow/envs/pangolin.yaml +++ b/workflow/envs/pangolin.yaml @@ -3,4 +3,5 @@ channels: - bioconda - nodefaults dependencies: - - pangolin =4.3.1 + - pangolin =4.3 + - snakemake-minimal=7.24.0 # TODO keep until https://github.com/bioconda/bioconda-recipes/pull/42192 and we can pin to 4.3.1 above From b8040317e40a37b15f5b5fb05ee2f05b9c59c77d Mon Sep 17 00:00:00 2001 From: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Date: Tue, 15 Oct 2024 10:51:23 +0200 Subject: [PATCH 4/4] Update spades.yaml --- workflow/envs/spades.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/envs/spades.yaml b/workflow/envs/spades.yaml index d88fde2c..32c7a4d3 100644 --- a/workflow/envs/spades.yaml +++ b/workflow/envs/spades.yaml @@ -3,4 +3,4 @@ channels: - bioconda - nodefaults dependencies: - - spades =3.15 + - spades =4.0