It is understood that you are not a retainer but an employee only. Even though your employment is for a fixed term, you will be covered by all the rules and regulations concerning employment of persons. A retainer is a person whose expert advice is taken as and when required. He will not regularly attend the office, but he visits the office only when his presence is required in the office. He will never ask for leave and will never follow the office timing. The fee paid is called a retainer fee, and that will come under the head of Professional fee. This is a service, and he can issue an invoice which may include GST. Since you have been allotted leaves, your status is not as a Consultant/Retainer but an employee.
The question of GST will not arise in your case because your relationship with the company is that of an employee and employer. Being an employee, your remuneration should be subjected to tax deduction at source under the head "Salaries" only. The TDS should be made as per section 192 and not u/s 194J. Section 194J is applicable for professionals, whereas the former is applicable for employees. It's worth referring to Wockhardt Hospitals Limited vs. Department Of Income Tax in which it was observed that the remuneration paid to doctors appointed as consultants was chargeable to tax under the head 'salaries' and liable for deduction of tax u/s. 192 of the Act, not under the provisions of section 194J of the Act.