Description

There are about 7 linting tests failing at the moment which we need to fix:

❌ Test failures:
files_unchanged - .github/CONTRIBUTING.md does not match the template
files_unchanged - assets/sendmail_template.txt does not match the template
files_unchanged - assets/nf-core-oncorefiner_logo_light.png does not match the template
files_unchanged - docs/images/nf-core-oncorefiner_logo_dark.png does not match the template
schema_params - Param snv_vcf from nextflow config not found in nextflow_schema.json
schema_params - Param sv_vcf from nextflow config not found in nextflow_schema.json
schema_params - Param custom_extra_files from nextflow config not found in nextflow_schema.json

Also, the module fastqc is present in 'modules.json' but the module files are missing.

And additional formatting issues raised by pre-commit.

Acceptance criteria

• Add CONTRIBUTING.md to list of files to ignore in the linting config.
• Fix sendmail_template.txt according to template.
• Add logo files to list of files to ignore in the linting config.
• Add missing params to schema.
• Remove fastqc.
• Fix formatting issues with pre-commit.
• There are no linting issues raised by the CI.