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Explicitly disable conda container profiles #2140

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merged 3 commits into from
Dec 23, 2022
Merged

Explicitly disable conda container profiles #2140

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5d95478
Explicitly disable conda in container profiles
jfy133 Dec 23, 2022
bb6ed95
Update CHANGELOG.md
jfy133 Dec 23, 2022
a09c060
Apply suggestions from code review
jfy133 Dec 23, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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 a container profile ([#2140](https://github.com/nf-core/tools/pull/2140))

### Linting

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5 changes: 5 additions & 0 deletions nf_core/pipeline-template/nextflow.config
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Expand Up @@ -102,6 +102,7 @@ profiles {
docker {
docker.enabled = true
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
Expand All @@ -113,27 +114,31 @@ profiles {
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
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