adjusted docs

Author: CaroAMN

docs/output.md

@@ -19,6 +19,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [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
+- [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
 
 ### NumorphIntensity
@@ -129,6 +130,19 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
   **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.
 
+### MultiQC
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `multiqc/`
+  - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser.
+  - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline.
+
+</details>
+
+**MultiQC** collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
 ### Pipeline information
 
 <details markdown="1">

docs/usage.md

@@ -51,12 +51,11 @@ The individual parameters are explained [here](###Analysisspecificparameters)
 
 ### Analysis specific parameters
 
-This section descripbes every parameter that can be set in the `parameter.csv`. In order that the pipeline runs correctly all named parameters need to be present in the parameter file and its recommended to use the provided parameter file (link). Every parameter has a default value that will be set if not otherwise defined in the `parameter.csv`.
+This section descripbes every parameter that can be set in the `parameter.csv`. In order for the pipeline to run correctly all named parameters need to be present in the parameter file and its recommended to use the provided parameter file (link). Every parameter has a default value that will be set if not otherwise defined in the `parameter.csv`.
 
 | Parameter                   | Description                                                                                                                                                                                                                                     |
 | --------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `darkfield_intensity`       | 1xn_channels; Constant darkfield intensity value (i.e. average intensity of image with nothing present). **Default: 101**                                                                                                                       |
-| `img_directory`             |                                                                                                                                                                                                                                                 |
 | `single_sheet`              | true, false; Whether a single sheet was used for acquisition                                                                                                                                                                                    |
 | `ls_width`                  | 1xn_channels interger. Light sheet width setting for UltraMicroscope II as percentage. **Default: 50**                                                                                                                                          |
 | `laser_y_displacement`      | [-0.5,0.5]; Displacement of light-sheet along y axis. Value of 0.5 means light-sheet center is positioned at the top of the image. **Default: 0**                                                                                               |
@@ -164,7 +163,7 @@ This section descripbes every parameter that can be set in the `parameter.csv`.
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/lsmquant --input ./samplesheet.csv --outdir ./results -profile docker
+nextflow run nf-core/lsmquant --input ./samplesheet.csv --outdir ./results -profile docker -work-dir ./work
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -178,6 +177,8 @@ work                # Directory containing the nextflow working files
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
+For this pipeline it is recommended to specify the location of the work directory as well with `-work-dir`. The directory will contain any nextflow working files which includes all in- and output files. The work directory will be larger than the input sample size. If you don't specify a location, the work directory will be created in the location from where the pipeline got started.
+
 If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file.
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.