From 5d954788ebec7810bc0b77b173ecb2d58d403465 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 23 Dec 2022 10:30:45 +0100 Subject: [PATCH 1/3] Explicitly disable conda in container profiles --- nf_core/pipeline-template/nextflow.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 5cbb076b46..cc591a54e5 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -102,6 +102,7 @@ profiles { docker { docker.enabled = true docker.userEmulation = true + conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false @@ -113,6 +114,7 @@ profiles { singularity { singularity.enabled = true singularity.autoMounts = true + conda.enabled = false docker.enabled = false podman.enabled = false shifter.enabled = false @@ -120,6 +122,7 @@ profiles { } podman { podman.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false shifter.enabled = false @@ -127,6 +130,7 @@ profiles { } shifter { shifter.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false @@ -134,6 +138,7 @@ profiles { } charliecloud { charliecloud.enabled = true + conda.enabled = false docker.enabled = false singularity.enabled = false podman.enabled = false From bb6ed953e593d4619aa25ceafba2074a464fe69d Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 23 Dec 2022 10:32:17 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index d8c5d89f5d..62eef56c6c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ - Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114)) - Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132)) +- Explicitly disable `conda` when using container profiles ([#2140](https://github.com/nf-core/tools/pull/2140)) ### Linting From a09c06099aecc9d88c5f9abe399fe810cde238d4 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 23 Dec 2022 10:35:00 +0100 Subject: [PATCH 3/3] Apply suggestions from code review --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 62eef56c6c..be6d5820d7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,7 @@ - Fix the syntax of github_output in GitHub actions ([#2114](https://github.com/nf-core/tools/pull/2114)) - Fix a bug introduced in 2.7 that made pipelines hang ([#2132](https://github.com/nf-core/tools/issues/2132)) -- Explicitly disable `conda` when using container profiles ([#2140](https://github.com/nf-core/tools/pull/2140)) +- Explicitly disable `conda` when a container profile ([#2140](https://github.com/nf-core/tools/pull/2140)) ### Linting