add shifter profile + docs

as suggested by @ewels in nf-core#824 (comment)

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
 

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: <!-- [e.g. Conda, Docker, Singularity, Podman or Charliecloud] -->
+- Engine: <!-- [e.g. Conda, Docker, Singularity, Podman, Shifter or Charliecloud] -->
 - version: <!-- [e.g. 1.0.0] -->
 - Image tag: <!-- [e.g. {{ cookiecutter.name_docker }}:1.0.0] -->
 

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,<docker/singularity/podman/charliecloud/conda/institute>
+    nextflow run {{ cookiecutter.name }} -profile test,<docker/singularity/podman/shifter/charliecloud/conda/institute>
     ```
 
     > 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 <institute>` 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
     <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
     ```bash
-    nextflow run {{ cookiecutter.name }} -profile <docker/singularity/podman/charliecloud/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
+    nextflow run {{ cookiecutter.name }} -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --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.

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`

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' }