From d998e788e7ab1953b07a98918b9316c13dae6c6c Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 29 Apr 2023 17:52:49 +0200 Subject: [PATCH 1/4] Typo tweaks and minor clarifications --- nf_core/pipeline-template/README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/README.md b/nf_core/pipeline-template/README.md index e2ca15a8e6..5ac65123ed 100644 --- a/nf_core/pipeline-template/README.md +++ b/nf_core/pipeline-template/README.md @@ -82,11 +82,11 @@ nextflow run {{ name }} \ {% if branded -%} -For more details, please refer to the [usage documentation](https://nf-co.re/{{ short_name }}/usage) and the [parameter documentation](https://nf-co.re/{{ short_name }}/parameters). +For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/{{ short_name }}/usage) and the [parameter documentation](https://nf-co.re/{{ short_name }}/parameters). ## Pipeline output -To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/{{ short_name }}/results) tab on the nf-core website pipeline page. +To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/{{ short_name }}/results) tab on the nf-core website pipeline page. For more details about the output files and reports, please refer to the [output documentation](https://nf-co.re/{{ short_name }}/output). From c94b08bf4deed7d46af9592286a390c47a2e4c1d Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 4 May 2023 07:17:28 +0200 Subject: [PATCH 2/4] GitPod base image: Always self-update to the latest version of Nextflow. --- CHANGELOG.md | 2 ++ nf_core/gitpod/gitpod.Dockerfile | 15 +++++++++------ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3c0792519..f0940d53b9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ ### General +- GitPod base image: Always self-update to the latest version of Nextflow. + # [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27] ### Template diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 417208a20d..252b9bd088 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -38,13 +38,16 @@ RUN conda config --add channels defaults && \ conda config --set channel_priority strict && \ conda install --quiet --yes --name base mamba && \ mamba install --quiet --yes --name base \ - nextflow=22.10.1 \ - nf-core \ - nf-test \ - black \ - prettier \ - pytest-workflow && \ + nextflow \ + nf-core \ + nf-test \ + black \ + prettier \ + pytest-workflow && \ mamba clean --all -f -y +# Update Nextflow +RUN nextflow self-update + # Install nf-core RUN python -m pip install . From 5cd0b867fa06b762762b97530c79aa5915a57a37 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Thu, 4 May 2023 07:23:29 +0200 Subject: [PATCH 3/4] GitPod config: Update Nextflow in init. Install pre-commit. --- .gitpod.yml | 1 + CHANGELOG.md | 3 ++- nf_core/gitpod/gitpod.Dockerfile | 1 + nf_core/pipeline-template/.gitpod.yml | 5 +++++ 4 files changed, 9 insertions(+), 1 deletion(-) diff --git a/.gitpod.yml b/.gitpod.yml index a93e660516..1cc63b197f 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -5,6 +5,7 @@ tasks: python -m pip install -e . python -m pip install -r requirements-dev.txt pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files diff --git a/CHANGELOG.md b/CHANGELOG.md index f0940d53b9..11bc0e1a69 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,7 +14,8 @@ ### General -- GitPod base image: Always self-update to the latest version of Nextflow. +- GitPod base image: Always self-update to the latest version of Nextflow. Add [pre-commit](https://pre-commit.com/) dependency. +- GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config. # [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27] diff --git a/nf_core/gitpod/gitpod.Dockerfile b/nf_core/gitpod/gitpod.Dockerfile index 252b9bd088..5fce2f055b 100644 --- a/nf_core/gitpod/gitpod.Dockerfile +++ b/nf_core/gitpod/gitpod.Dockerfile @@ -43,6 +43,7 @@ RUN conda config --add channels defaults && \ nf-test \ black \ prettier \ + pre-commit \ pytest-workflow && \ mamba clean --all -f -y diff --git a/nf_core/pipeline-template/.gitpod.yml b/nf_core/pipeline-template/.gitpod.yml index 85d95ecc8e..25488dcc08 100644 --- a/nf_core/pipeline-template/.gitpod.yml +++ b/nf_core/pipeline-template/.gitpod.yml @@ -1,4 +1,9 @@ image: nfcore/gitpod:latest +tasks: + - name: Update Nextflow and setup pre-commit + command: | + pre-commit install --install-hooks + nextflow self-update vscode: extensions: # based on nf-core.nf-core-extensionpack From 5e054c260228e25f0848da30af0491b4b90e073d Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 4 May 2023 21:28:56 +0100 Subject: [PATCH 4/4] Remove cleanup=true from test_full.config --- CHANGELOG.md | 3 +++ nf_core/pipeline-template/conf/test_full.config | 2 -- nf_core/pipeline-template/docs/usage.md | 6 +++--- 3 files changed, 6 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d3c0792519..fb5e81e6e2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,9 @@ ### Template +- Remove `cleanup = true` from `test_full.config` in pipeline template +- Fix usage docs for specifying `params.yaml` + ### Linting - Warn if container access is denied ([#2270](https://github.com/nf-core/tools/pull/2270)) diff --git a/nf_core/pipeline-template/conf/test_full.config b/nf_core/pipeline-template/conf/test_full.config index 46b165a910..d92692fa94 100644 --- a/nf_core/pipeline-template/conf/test_full.config +++ b/nf_core/pipeline-template/conf/test_full.config @@ -10,8 +10,6 @@ ---------------------------------------------------------------------------------------- */ -cleanup = true - params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' diff --git a/nf_core/pipeline-template/docs/usage.md b/nf_core/pipeline-template/docs/usage.md index 73e1132541..e89c2a7332 100644 --- a/nf_core/pipeline-template/docs/usage.md +++ b/nf_core/pipeline-template/docs/usage.md @@ -61,7 +61,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run {{ name }} --input samplesheet.csv --outdir --genome GRCh37 -profile docker +nextflow run {{ name }} --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -80,7 +80,8 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. > ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). -> The above pipeline run specified with a params file in yaml format: + +The above pipeline run specified with a params file in yaml format: ```bash nextflow run {{ name }} -profile docker -params-file params.yaml @@ -92,7 +93,6 @@ with `params.yaml` containing: input: './samplesheet.csv' outdir: './results/' genome: 'GRCh37' -input: 'data' <...> ```