From ca568d07446be8bc667066e46a9d315d5a513fe0 Mon Sep 17 00:00:00 2001 From: Ezra Herman <55948629+ezherman@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:07:20 +0000 Subject: [PATCH 1/3] Set Snakemake to v7.32.0 --- .github/workflows/main.yml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 5d28ca0..d80035c 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -25,7 +25,7 @@ jobs: steps: - uses: actions/checkout@v2 - name: Lint workflow - uses: snakemake/snakemake-github-action@v1.24.0 + uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c with: directory: . snakefile: workflow/Snakefile @@ -40,15 +40,15 @@ jobs: - uses: actions/checkout@v2 - name: Test workflow - uses: snakemake/snakemake-github-action@v1.24.0 + uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c with: directory: .test snakefile: workflow/Snakefile - args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp" + args: "--use-conda --show-failed-logs --cores 1 --conda-cleanup-pkgs cache --all-temp" - name: Test report - uses: snakemake/snakemake-github-action@v1.24.0 + uses: ezherman/snakemake-github-action@5027c0e706ada924ab91e0501bd92185fc98de3c with: directory: .test snakefile: workflow/Snakefile - args: "--report report.zip" \ No newline at end of file + args: "--report report.zip" From c8eac58ed709ca0eaaa5cfa4190f22284b0077bf Mon Sep 17 00:00:00 2001 From: Ezra Herman <55948629+ezherman@users.noreply.github.com> Date: Thu, 21 Dec 2023 17:14:55 +0000 Subject: [PATCH 2/3] Change yaml location --- workflow/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 7ddaaa0..c38c7dc 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -5,7 +5,7 @@ rule touch: output: "file.txt" - conda: "../envs/empty.yaml" + conda: "envs/empty.yaml" log: "logs/touch.log" shell: "touch {output}" From 76ceecd0414d1e340a5c40ada431c0a9c3b0c911 Mon Sep 17 00:00:00 2001 From: ezherman Date: Thu, 21 Dec 2023 17:20:31 +0000 Subject: [PATCH 3/3] snakefmt --- workflow/Snakefile | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index c38c7dc..46dc637 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -1,11 +1,15 @@ -# Main entrypoint of the workflow. -# Please follow the best practices: +# Main entrypoint of the workflow. +# Please follow the best practices: # https://snakemake.readthedocs.io/en/stable/snakefiles/best_practices.html, -# in particular regarding the standardized folder structure mentioned there. +# in particular regarding the standardized folder structure mentioned there. + rule touch: - output: "file.txt" - conda: "envs/empty.yaml" - log: "logs/touch.log" + output: + "file.txt", + conda: + "envs/empty.yaml" + log: + "logs/touch.log", shell: "touch {output}"