Apply suggestions from code review

Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>

Author: CaroAMN

.nf-core.yml

@@ -9,4 +9,7 @@ template:
   name: lsmquant
   org: nf-core
   outdir: .
+  skip_features:
+  	- fastqc
+  	- igenomes
   version: 1.0.0

README.md

@@ -51,7 +51,7 @@ The pipeline consists of two major workflows `preprocessing` and the `full` work
 
 ### Preprocessing
 
-Preprocessing is performed on raw 2D single-channel 16-bit `.tif` images produced by a light sheet microscope. Three individual steps are perfomed :
+Preprocessing is performed on raw 2D single-channel 16-bit `.tif` images produced by a light sheet microscope. Three individual steps are performed:
 
 - **Intensity adjustments** to correct for the Gaussian shape of the lightsheet and intensity differences between adjacent tiles
 - **Image channel alignment** using a 2D rigid approach or a nonlinear 3D approach using Elastix.
@@ -63,7 +63,7 @@ Quantification of cell-nuclei is performed using a 3D-Unet. It is performed on t
 
 ### ARA Registration
 
-Optionally registration to the Allen Refernce Atlas (ARA) for functional brain region annotation can be perfomed before segmentation.
+Optional registration to the Allen Reference Atlas (ARA) for functional brain region annotation can be perfomed before segmentation.
 This includes the following two steps:
 
 - Downsampling of the high resolution stitched images
@@ -78,14 +78,14 @@ To run the pipeline you need to provide a samplesheet with your data in the foll
 
 `samplesheet.csv`
 
-```bash
+```csv
 sample_id,img_directory,parameter_file
 TEST1,path/to/image-files,path/to/parameter/file.csv
 ```
 
-The parameter csv file includes sample specific parameters that are used for processing the given data.It needs to follow a specific structure.
+The parameter csv file includes sample specific parameters that are used for processing the given data. It needs to follow a specific structure.
 
-Please get the basic tempalte file here ( include maybe link to template csv which can be found in the repo ?)
+Please get the basic template file [here](../assets/params_template_lsmquant.csv).
 `parametersheet.csv`
 
 Now, you can run the pipeline using:

docs/output.md

@@ -12,15 +12,15 @@ 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:
 
-- [NumorphIntensity](#numorphintensity) - Mesures intensity parameters for illumination correction
+- [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
 - [NumorphResample](#numorphresample) - Generate downsamppled images
-- [NumorphRegister](#numorphregister) - Performs registartion to the Allen Reference Atlas (ARA)
-- [Numorph3DUnet](#numorph3dunet) - Perfomrs cell-nuclei segmentation and quantification
-- [Mat2JSON] (#mat3json) - Converts `.mat`files to JSON
+- [NumorphRegister](#numorphregister) - Performs registration to the Allen Reference Atlas (ARA)
+- [Numorph3DUnet](#numorph3dunet) - Performs cell-nuclei segmentation and quantification
+- [Mat2JSON](#mat2json) - Converts `.mat`files to JSON
 - [MultiQC](#MultiQC) Aggregate report describing workflow run and tools used from the whole pipeline.
-- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
+- [Pipeline information](#pipeline-information) - Reports the metrics generated during the workflow execution
 
 ### NumorphIntensity
 
@@ -30,7 +30,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - `Sample_id/intensity/results`
   - `NM_variables.mat`: Contains input and calculated parameters
   - `samples/`
-    - `[channel]_x_y_z.tif`: Image comparing raw and adjusted image tiles for respective channel. Example for each tile of the middel z slice
+    - `[channel]_x_y_z.tif`: Image comparing raw and adjusted image tiles for respective channel. Example for each tile of the middle z slice
     - `flatfield_*.png`: Flatfield correction heatmap for each channel
     - `tile_adj_*.png`: Heatmap of tile positions displaying illumination correction factor for each tile
     - `y_adj_*.png`: Intensity correction factors along the Y-axis(using intensity profiles specifically for the LaVision Ultramicroscope II)