From b8c5c449f81ba9c08bcdb68a099318eca1e64066 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 17 Oct 2024 18:31:12 +0200 Subject: [PATCH] chore: checkout full history for formatting (#668) * chore: checkout full history for formatting * force latest pangolin * work around pangolin dependency issues * Update spades.yaml --------- Co-authored-by: Alexander Thomas <77535027+alethomas@users.noreply.github.com> Co-authored-by: Alex Thomas --- .github/workflows/main.yml | 2 ++ workflow/envs/pangolin.yaml | 1 + workflow/envs/spades.yaml | 2 +- 3 files changed, 4 insertions(+), 1 deletion(-) 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: diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml index f6a26ad4..42265aca 100644 --- a/workflow/envs/pangolin.yaml +++ b/workflow/envs/pangolin.yaml @@ -4,3 +4,4 @@ channels: - nodefaults dependencies: - 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 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