From 3096adc397ef0a9d2c45f47497c5cfe66a497367 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 11 May 2021 11:52:30 +0200 Subject: [PATCH 1/2] Fix review comments from @maxulysse in nf-core/tools#1066 --- CHANGELOG.md | 2 +- nf_core/pipeline-template/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f8b72fb213..36ba54e3a7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,7 +40,7 @@ * Fix bug in nf-core lint config skipping for the `nextflow_config` test [[#1019](https://github.com/nf-core/tools/issues/1019)] * New `-k`/`--key` cli option for `nf-core lint` to allow you to run only named lint tests, for faster local debugging * Merge markers lint test - ignore binary files, allow config to ignore specific files [[#1040](https://github.com/nf-core/tools/pull/1040)] -* New lint test to check if params in `nextflow config` are mentioned in `main.nf` [[#1038](https://github.com/nf-core/tools/issues/1038)] +* New lint test to check if all defined pipeline parameters are mentioned in `main.nf` [[#1038](https://github.com/nf-core/tools/issues/1038)] * Added fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)] * Added pipeline schema lint checks for missing parameter description and parameters outside of groups [[#1017](https://github.com/nf-core/tools/issues/1017)] diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index 311472a287..87c48a2c30 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -19,7 +19,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool ## Quick Start -1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=21.04.0`) +1. Install [`nextflow`](https://nf-co.re/usage/installation) (`>=20.04.0`) 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))_ From d731d3dee1752d3b19a93801e5171733cfa8bc68 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Tue, 11 May 2021 12:03:00 +0200 Subject: [PATCH 2/2] Add docs for building docker image with specific NXF_VER --- README.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/README.md b/README.md index 8e7b7206bb..ba57848a74 100644 --- a/README.md +++ b/README.md @@ -113,6 +113,14 @@ nf-core list You can use docker image tags to specify the version you would like to use. For example, `nfcore/tools:dev` for the latest development version of the code, or `nfcore/tools:1.14` for version `1.14` of tools. If you omit this, it will default to `:latest`, which should be the latest stable release. +If you need a specific version of Nextflow inside the container, you can build an image yourself. +Clone the repo locally and check out whatever version of nf-core/tools that you need. +Then build using the `--build-arg NXF_VER` flag as follows: + +```bash +docker build -t nfcore/tools:dev . --build-arg NXF_VER=20.04.0 +``` + ### Development version If you would like the latest development version of tools, the command is: