Merge branch 'dev' into add-stub-to-modules-template

.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

CHANGELOG.md

@@ -4,7 +4,9 @@
 
 ### Template
 
-- Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277)
+- Remove `cleanup = true` from `test_full.config` in pipeline template
+- Fix usage docs for specifying `params.yaml`
+- Added stub in modules template ([#2277])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk]
 
 ### Linting
 
@@ -16,6 +18,9 @@
 
 ### General
 
+- 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]
 
 ### Template

nf_core/gitpod/gitpod.Dockerfile

@@ -38,13 +38,17 @@ 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 \
+        pre-commit \
+        pytest-workflow && \
     mamba clean --all -f -y
 
+# Update Nextflow
+RUN nextflow self-update
+
 # Install nf-core
 RUN python -m pip install .

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

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).
 

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'

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 <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 <file>`.
 
 > ⚠️ Do not use `-c <file>` 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'
 <...>
 ```