apply suggestions from code review, typos

.nf-core.yml

@@ -10,6 +10,6 @@ template:
   org: nf-core
   outdir: .
   skip_features:
-  	- fastqc
-  	- igenomes
+    - fastqc
+    - igenomes
   version: 1.0.0

CHANGELOG.md

@@ -43,6 +43,6 @@ local subworkflows:
 
 ### `Dependencies`
 
-Custom numorph container `numorphpreprocessing`, `numorphanalyze`, `mat2json`, and `numorph3dunet`are on the nf-core quay io repository. Compiled matlab application [numorph_preprocessing](https://github.com/CaroAMN/numorph_preprocessing), [mat2json](https://github.com/CaroAMN/mat2json) and the source code for the [3Dunet](https://github.com/CaroAMN/numorph_3dunet) python package are public repositories. The source code of the tools are found here [NuMoprh_dev](https://github.com/CaroAMN/Numorph_dev/tree/main)
+Custom numorph container `numorphpreprocessing`, `numorphanalyze`, `mat2json`, and `numorph3dunet`are on the nf-core quay io repository. Compiled matlab application [numorph_preprocessing](https://github.com/CaroAMN/numorph_preprocessing), [mat2json](https://github.com/CaroAMN/mat2json) and the source code for the [3Dunet](https://github.com/CaroAMN/numorph_3dunet) python package are public repositories. The source code of the tools are found here [NuMorph_dev](https://github.com/CaroAMN/Numorph_dev/tree/main)
 
 ### `Deprecated`

docs/output.md

@@ -12,6 +12,7 @@ The directories listed below will be created in the results directory after the
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
+- [StageFiles](#stagefiles) - Stageing images from the input directory into the workdirectory.
 - [NumorphIntensity](#numorphintensity) - Measures intensity parameters for illumination correction
 - [NumorphAlign](#numorphalign) - Performs 2D rigid or 3D non-linear channel alignment
 - [NumorphStitch](#numoprhstitch) - Performs 2D iterative stitching of image tiles
@@ -22,6 +23,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [MultiQC](#MultiQC) Aggregate report describing workflow run and tools used from the whole pipeline.
 - [Pipeline information](#pipeline-information) - Reports the metrics generated during the workflow execution
 
+### StageFiles
+
+This process stages the image files from the input directory to the pipeline's work directory. This step is necessary to avoid duplication of input data in the work directory, as the processes **NumorphIntensity**, **NumorphAlign**, and **NumorphStitch** require the same input data.
+
 ### NumorphIntensity
 
 <details markdown="1">
@@ -94,15 +99,19 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 </details>
 
-**NumorphResample** downsamples the image resolition to macht the Allen Reference Atlas resolution befor registration.
+**NumorphResample** downsamples the image resolution to macht the Allen Reference Atlas resolution befor registration.
 
 ### NumorphRegister
 
 <details markdown="1">
 <summary>Output files</summary>
 
-- `Sample_id/results` - `NM_variables.mat`: Contains input and calculated parameters - `registered/*_MOV_*.nii`: Moving image from registration - `registered/*_REF_*.nii`: Reference imgae from registration - `variables/reg_params.mat`: Registration parameters
-</details>
+- `Sample_id/results`:
+  - `NM_variables.mat`: Contains input and calculated parameters
+  - `registered/*_MOV_*.nii`: Moving image from registration
+  - `registered/*_REF_*.nii`: Reference image from registration
+  - `variables/reg_params.mat`: Registration parameters
+  </details>
 
 **NumorphRegister** performs image registration to the Allen Reference Atlas.
 
@@ -128,7 +137,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
   - `*.json/*.csv`: Converted mat file
   </details>
 
-  **Mat2JSON** converts a given `.mat`file into a `CSV` if the data is stored as a table datastructure or a `JSON` for other nested datastructures.
+  **Mat2JSON** converts a given `.mat`file into a `CSV` if the data is stored as a table data structure or a `JSON` for other nested data structures.
 
 ### MultiQC
 

docs/usage.md

@@ -2,8 +2,6 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
-
 ## Samplesheet input
 
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
@@ -262,7 +260,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `wave`
   - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
-  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
+  - This profile is not available for nf-core/lsmquant
 
 ### `-resume`
 

modules/local/stagefiles/meta.yml

@@ -1,14 +1,14 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "stagefiles"
-description: A helper modules to stage files from a directory into the work directory
+description: A helper module to stage files from a directory into the work directory
 keywords:
   - stageing
   - empty module
   - files
   - helper
 tools:
   - "stagefiles":
-      description: "this is an empty modules for staging files into the work directory of a nextflow pipeline"
+      description: "This is an empty module for staging files into the work directory of the nf-core/lsmquant pipeline."
       homepage: ""
       documentation: ""
       tool_dev_url: ""

nextflow.config

@@ -9,7 +9,6 @@
 // Global default params, used in configs
 params {
 
-    // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                       = null
     stage                       = 'preprocessing'

subworkflows/local/araregistration/meta.yml

@@ -1,6 +1,5 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json
 name: "araregistration"
-## TODO nf-core: Add a description of the subworkflow and list keywords
 description: Image registration of 2D stitched images to the Allan reference atlas
 keywords:
   - registration

subworkflows/local/numorph_preprocessing/meta.yml

@@ -6,7 +6,6 @@ keywords:
   - alignment
   - stitching
   - tiff
-
 components:
   - numorphintensity
   - numorphalign

tests/nextflow.config

@@ -4,8 +4,6 @@
 ========================================================================================
 */
 
-// TODO nf-core: Specify any additional parameters here
-// Or any resources requirements
 params {
     modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/lsmquant'

workflows/lsmquant.nf

@@ -23,7 +23,6 @@ include { MULTIQC                } from '../modules/nf-core/multiqc'
 
 
 
-
 workflow LSMQUANT {
 
     take: