Reorganizes the schema

[FriederikeHanssen]

This PR aims to improve the order of the Nextflow schema by reorganizing sections and adding defaults for enhanced readability.

Changes

• Reorganized schema sections: Moved input_output_options to the top for better visibility
• Added defaults to required parameters:
  • genomes_base: s3://nf-core-awsmegatests/rnafusion/references
  • genome_gencode_version: 46
  • genome: GRCh38
• Consolidated options: Merged compression_options into alignment_options and add additional alignment related parameters
• Move all reference related inputs to the reference section

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[maxulysse]

CHANGELOG?

[atrigila]

Thanks for the more logical reorganization.
I might be missing something. I understand that you consolidated options but I wasn't able to find the "additional alignment related parameters"? Apart from that LGTM, after fixing linting and updating changelog.

[FriederikeHanssen]

sorry. I just meant that i rename the section "Alignment compression" to "alignment" and then moved these parameters into it and out from the generic bottom section:

rnafusion/nextflow_schema.json

Lines 151 to 194 in 047aa6b

	"alignment_options": {
	"title": "Alignment options",
	"type": "object",
	"fa_icon": "fas fa-align-center",
	"properties": {
	"cram": {
	"type": "boolean",
	"description": "Option to compress BAM files to CRAM. Output CRAM files instead of BAM files.",
	"fa_icon": "fas fa-cut"
	},
	"star_limit_bam_sort_ram": {
	"type": "integer",
	"description": "The maximum amount of RAM to use for sorting the BAM file in STAR. Should by in bits. Setting this value to `0` will use the default amount of STAR.",
	"fa_icon": "fas fa-toolbox",
	"minimum": 0
	},
	"star_ignore_sjdbgtf": {
	"type": "boolean",
	"description": "Whether to ignore the GTF in STAR alignment",
	"hidden": true,
	"fa_icon": "fas fa-toolbox",
	"help_text": "Setting false will use GTF file for STAR alignment"
	},
	"read_length": {
	"type": "integer",
	"fa_icon": "far fa-file-code",
	"description": "The length of the reads provided to the pipeline. This is used for the '--sjdbOverhang' option of STAR as read_length - 1. Providing 1 to this option will disable overhang handling.",
	"default": 100,
	"minimum": 1
	},
	"seq_platform": {
	"type": "string",
	"description": "Sequencing platform, used to fill in read group PL tag in the BAM header",
	"fa_icon": "fas fa-toolbox",
	"help_text": "This will reported in the BAM header as PL."
	},
	"seq_center": {
	"type": "string",
	"description": "Sequencing center, used to fill in read group CN tag in the BAM header",
	"fa_icon": "fas fa-toolbox",
	"help_text": "This will reported in the BAM header as CN"
	}
	}
	},