Software is a fundamental pillar of modern scientific research, across all fields and disciplines. However, there is a general lack of adequate means to archive, reference and cite software. In this talk, we will survey the main issues that make this task difficult, ranging from the specificity of the persistent identifiers needed for reproducibility to the complexity of determining software authorship and authority, especially for long running projects, which are needed for proper software attribution and credit. We report on recent contributions to the ongoing efforts to develop proper processes, guidelines and recommendations for software reference and software citation, building upon the internal experience of Inria and the emerging Software Heritage infrastructure.