In my teaching at this level, I have always emphasized research design. This begins with each student creating a question that is actually "researchable," and learning about methods that would appropriate for collecting and analyzing data to address that question.

I find that getting students to think about what they want to accomplish, right from the beginning of their instruction, makes it easier for them to relate to the skills that they need to master.

Hello, I am an SME in developing researcher's competencies in doctorate school.  How can I help you to change (the sometime frustrating) experience. Developing research competencies takes time, strategies, organization, dedication, focus, and somehow coding. Feel free to contact me for collaboration.

Iberkis

I have taught research methods here twice, for both doctoral and masters-level students. There are challenges, to be sure.How can I help?

I can humbly but heartily recommend my E-book, "How to do Research: Today's Tips and Tools".

A screening of www.researchgate.net/project/Researcher-Skills-Improvement may lead you to some valuable links to follow up.

Be aware that much advice on the internet about writing "research" papers is directed to high school pupils who will not be undertaking primary research, but this is the goal of doctoral research. 

School papers will only review existing material, and not involve the creation of a deep research question, the collecting and re-collection of primary data, data analysis, the development of a thesis-theme, the writing of an integrated thesis-book, an original, significant (and hopefully useful) contribution to our knowledge.

So the missing skills include critical and creative thinking, data collecting and analysis skills, and deep thinking. 

I recommend also, to have a look at the website of Dr. Inger Mewburn.

However, beware that research is not research and doctorate school is not doctorate school. In other words: it makes a difference whether you want to supervise researchers in the natural sciences, in the social sciences, or else.

Note that I am deliberately using the term "supervise". IMHO the concept and model of a "school" is inappropriate for learning and training to become a good "researcher" in any discipline, even if we are using the same familiar terms "learning", "training", "teaching", etc.

Surely can you set up and offer students school-like programmes during their PhD research, but these will have nothing to do with or have a substantial influence on the meta-cognitive and meta-technical capabilities that are supposed to be so characteristics of good scientists (see above). And the basic "skills" should have been taught and learned already in the preceding years at the university.

The appropriate models you will find in e.g. medicine, music, psychotherapy, and many other fields, where there is a closed interactive cycle between supervisor and supervisee in real research of a specific type. Research for real isn't the same as the industrial production of some good on the basis of prescribed knowledge and rules.

https://thesiswhisperer.com/

https://researchers.anu.edu.au/researchers/mewburn-i