From b524d554b1f5706b77629e5649ea926413813165 Mon Sep 17 00:00:00 2001 From: Max Date: Fri, 15 Jan 2021 10:17:53 +0100 Subject: [PATCH 1/2] same here. singularity is depricated using new `container` --- {{ cookiecutter.repo_name }}/workflow/rules/common.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/{{ cookiecutter.repo_name }}/workflow/rules/common.smk b/{{ cookiecutter.repo_name }}/workflow/rules/common.smk index 09feabd..a361616 100644 --- a/{{ cookiecutter.repo_name }}/workflow/rules/common.smk +++ b/{{ cookiecutter.repo_name }}/workflow/rules/common.smk @@ -3,7 +3,7 @@ import pandas as pd # this container defines the underlying OS for each job when using the workflow # with --use-conda --use-singularity -singularity: "docker://continuumio/miniconda3" +container: "docker://continuumio/miniconda3" ##### load config and sample sheets ##### From 19704246dc36923499d1d9b89ab930212ca15166 Mon Sep 17 00:00:00 2001 From: Max Date: Fri, 15 Jan 2021 10:20:05 +0100 Subject: [PATCH 2/2] using container in Snakefile --- {{ cookiecutter.repo_name }}/workflow/Snakefile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/{{ cookiecutter.repo_name }}/workflow/Snakefile b/{{ cookiecutter.repo_name }}/workflow/Snakefile index 962c0d6..6e781d9 100644 --- a/{{ cookiecutter.repo_name }}/workflow/Snakefile +++ b/{{ cookiecutter.repo_name }}/workflow/Snakefile @@ -5,7 +5,7 @@ report: "report/workflow.rst" # Allow users to fix the underlying OS via singularity. -singularity: "docker://continuumio/miniconda3" +container: "docker://continuumio/miniconda3" rule all: