Add agat sp merge annotations

[Leila011]

Description

• add agat_sp_merge_annotations
• handle multiple inputs

Issue ticket number

Closes #xxxx

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[DriesSchaumont]

Could you test if the following works?
A couple of things here:

1. If you set an environment variable as part of a composite command instead of on a separate line, it is only applied for the commands on that line (here IFS is only used by read, so no need to use unset afterwards)
2. The ${array[@]} syntax can be used to output an array which is seprated by spaces (space is the default separator, this can be adjusted)

Suggested change

	input_files=""
	IFS=";" read -ra file_names <<< "$par_gff"
	for file in "${file_names[@]}"; do
	input_files+="--gff $file "
	done
	unset IFS
	# run agat_sp_merge_annotations
	agat_sp_merge_annotations.pl \
	$input_files \
	-o "$par_output" \
	${par_config:+--config "${par_config}"}
	IFS=";" read -ra file_names <<< "$par_gff"
	# run agat_sp_merge_annotations
	agat_sp_merge_annotations.pl \
	$input_files \
	-o "$par_output" \
	${file_names[@]} \
	${par_config:+--config "${par_config}"}

[Leila011]

it does not, the input should be in this format: --gff input1.gff --gff input2.gff

[emmarousseau]

Made some minor formatting changes to config