I am currently working on my thesis and I am submitting a part of my thesis as a paper to a journal (same text no rephrasing in some parts). I believe the journal review takes about four to six months before it is published and my thesis will be published on my university website before that. When they check for plagiarism and they find a match between my paper and my thesis, will they reject it?
It is only (self-)plagiarism when you do not indicate that some text is being reused.
So there is a simple remedy: Add to your thesis some text that indicates which parts have been submitted where. This could be formulated for example as:
This chapter has been submitted to journal as authors, title
The best course of action here is to disclose that part of the work is being submitted for publication in the thesis. In fact, this is encouraged at my institution. It will make your thesis stronger if findings have been peer reviewed and the examiners will recognise that it has been deemed publication quality. One of their goals is to assess whether it is an original finding which a publication would support.
As for self-citation and self-plagiarism, that is a very difficult issue and some fields take presenting the same work without attributing the prior source very seriously. Consult your advisor for what is acceptable in your field. However, generally what you need to avoid is:
- Submitting the same work for publication in different journals
- Submitting the same work to fulfil the requirements of different degrees (e.g., Masters and PhD).
- Submitting the work of others (even coauthors) for your thesis.
I don't think including sections in both an article and thesis breaches these necessarily and may be acceptable in some fields. Thesis by publication is also becoming more widely acceptable. However, you do need to ensure that it is clear what your contribution to a publication was if it included verbatim in your thesis if there were coauthors (and their contributions are acknowledged and disclosed). Afterall, it is your work that is being assessed to fulfil your degree.