Fix typos (second round)

CHANGELOG.md

@@ -528,7 +528,7 @@ _In addition, `-r` / `--revision` has been changed to a parameter that can be pr
 - 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.
 - Refgenie: Create `nxf_home/nf-core/refgenie_genomes.config` path if it doesn't exist ([#2312](https://github.com/nf-core/tools/pull/2312))
-- Add CI tests to test running a pipeline whe it's created from a template skipping different areas
+- Add CI tests to test running a pipeline when it's created from a template skipping different areas
 
 ## [v2.8 - Ruthenium Monkey](https://github.com/nf-core/tools/releases/tag/2.8) - [2023-04-27]
 
@@ -1209,7 +1209,7 @@ This marks the first Nextflow DSL2-centric release of `tools` which means that s
 ## [v1.13.2 - Copper Crocodile CPR :crocodile: :face_with_head_bandage:](https://github.com/nf-core/tools/releases/tag/1.13.2) - [2021-03-23]
 
 - Make module template pass the EC linter [[#953](https://github.com/nf-core/tools/pull/953)]
-- Added better logging message if a user doesn't specificy the directory correctly with `nf-core modules` commands [[#942](https://github.com/nf-core/tools/pull/942)]
+- Added better logging message if a user doesn't specify the directory correctly with `nf-core modules` commands [[#942](https://github.com/nf-core/tools/pull/942)]
 - Fixed parameter validation bug caused by JSONObject [[#937](https://github.com/nf-core/tools/issues/937)]
 - Fixed template creation error regarding file permissions [[#932](https://github.com/nf-core/tools/issues/932)]
 - Split the `create-lint-wf` tests up into separate steps in GitHub Actions to make the CI results easier to read

nf_core/pipeline-template/conf/base.config

@@ -20,7 +20,7 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
+    // NOTE - Please try and reuse the labels below as much as possible.
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.

nf_core/pipeline-template/docs/usage.md

@@ -116,7 +116,7 @@ First, go to the [{{ name }} releases page](https://github.com/{{ name }}/releas
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. {% if multiqc %}For example, at the bottom of the MultiQC reports.{% endif %}
 
-To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
+To further assist in reproducibility, you can use share and reuse [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
 :::tip
 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.

nf_core/pipelines/refgenie.py

@@ -144,7 +144,7 @@ def update_config(rgc):
 
     This function is executed after running 'refgenie pull <genome>/<asset>'
     The refgenie config file is transformed into a nextflow.config file, which is used to
-    overwrited the 'refgenie_genomes.config' file.
+    overwrite the 'refgenie_genomes.config' file.
     The path to the target  config file is inferred from the following options, in order:
 
     - the 'nextflow_config' attribute in the refgenie config file

nf_core/utils.py

@@ -721,7 +721,7 @@ def parse_anaconda_licence(anaconda_response, version=None):
         license = re.sub(r"GPL \(([^\)]+)\)", r"GPL \1", license)
         license = re.sub(r"GPL\s*v", "GPL v", license)  # Normalise whitespace to one space between GPL and v
         license = re.sub(r"\s*(>=?)\s*(\d)", r" \1\2", license)  # Normalise whitespace around >= GPL versions
-        license = license.replace("Clause", "clause")  # BSD capitilisation
+        license = license.replace("Clause", "clause")  # BSD capitalisation
         license = re.sub(r"-only$", "", license)  # Remove superfluous GPL "only" version suffixes
         clean_licences.append(license)
     return clean_licences

tests/pipelines/test_download.py

@@ -516,7 +516,7 @@ def test_singularity_image_filenames(self, tmp_path):
         result = download_obj.singularity_image_filenames("nf-core/ubuntu:20.04")
         assert result[0].endswith("/cachedir/nf-core-ubuntu-20.04.img")
 
-        ## Test phase III: Container wil lbe cached but also copied to out_path
+        ## Test phase III: Container will be cached but also copied to out_path
         # out_path: str, Path to cache
         # cache_path: str, Path to cache
         download_obj.container_cache_utilisation = "copy"