diff --git a/CHANGELOG.md b/CHANGELOG.md index a34bdd5d9b..7be5ea2dc0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ ### Template -* Added a profile to support the [Charliecloud container engine](https://hpc.github.io/charliecloud/) [[#824](https://github.com/nf-core/tools/issues/824)] +* Added profiles to support the [Charliecloud](https://hpc.github.io/charliecloud/) and [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) container engines [[#824](https://github.com/nf-core/tools/issues/824)] ### Linting diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md index db06c6ae7e..7f71baaa90 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/.github/ISSUE_TEMPLATE/bug_report.md @@ -55,7 +55,7 @@ Have you provided the following extra information/files: ## Container engine -- Engine: +- Engine: - version: - Image tag: diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md index 6443f8acbe..fea0200122 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/README.md @@ -21,12 +21,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool 1. Install [`nextflow`](https://nf-co.re/usage/installation) -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ 3. Download the pipeline and test it on a minimal dataset with a single command: ```bash - nextflow run {{ cookiecutter.name }} -profile test, + nextflow run {{ cookiecutter.name }} -profile test, ``` > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. @@ -36,7 +36,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool ```bash - nextflow run {{ cookiecutter.name }} -profile --input '*_R{1,2}.fastq.gz' --genome GRCh37 + nextflow run {{ cookiecutter.name }} -profile --input '*_R{1,2}.fastq.gz' --genome GRCh37 ``` See [usage docs](https://nf-co.re/{{ cookiecutter.short_name }}/usage) for all of the available options when running the pipeline. diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md index 2e7fb1485e..15aa301742 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/docs/usage.md @@ -71,11 +71,14 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof * `podman` * A generic configuration profile to be used with [Podman](https://podman.io/) * Pulls software from Docker Hub: [`{{ cookiecutter.name_docker }}`](https://hub.docker.com/r/{{ cookiecutter.name_docker }}/) +* `shifter` + * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) + * Pulls software from Docker Hub: [`{{ cookiecutter.name_docker }}`](https://hub.docker.com/r/{{ cookiecutter.name_docker }}/) * `charliecloud` - * A generic configuration profile to be used with [`Charliecloud`](https://hpc.github.io/charliecloud/) + * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) * Pulls software from Docker Hub: [`{{ cookiecutter.name_docker }}`](https://hub.docker.com/r/{{ cookiecutter.name_docker }}/) * `conda` - * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman or Charliecloud. + * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. * A generic configuration profile to be used with [Conda](https://conda.io/docs/) * Pulls most software from [Bioconda](https://bioconda.github.io/) * `test` diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config index 364b95ca9d..b107284482 100644 --- a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config +++ b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config @@ -74,6 +74,9 @@ profiles { podman { podman.enabled = true } + shifter { + shifter.enabled = true + } charliecloud { includeConfig 'conf/charliecloud.config' } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' }