journal_manuscript_adaptation v1.0.0

name: "journal_manuscript_adaptation" description: "Adapt a finished manuscript to a specific target journal before submission: study 8 to 12 recent papers in that journal, build a journal profile covering scope, article type, structure, length, abstract form, and citation habits, map every required change without altering findings, revise title, abstract, framing, and section order to fit, and run a scored pre-submission fit check. Use when a journal has been chosen, after a desk rejection for fit, or before moving a paper to a second journal. Distinct from peer_review_rebuttal, which handles replies after review." metadata: { "includeInPrompt": true }

Journal Manuscript Adaptation

Purpose

Turn a finished draft into a submission that looks like it was written for the journal it is going to. Editors screen for fit before they send a paper out for review. Out of scope topic, wrong article type, wrong length, wrong abstract form, and ignored author guidelines are common desk rejection reasons that have nothing to do with whether the work is good. This skill separates two jobs that authors often blur: keep the science exactly as it is, and change everything about presentation that the target journal expects to be different.

Workflow

1. Lock the findings first. Before any adaptation, write a one page findings lock: research question, design, sample or data source, primary result with its numbers as reported, secondary results, and the claims the authors will and will not make. Save it and treat it as read only. Every later edit is checked against it. If an adaptation idea would need a new number, a stronger claim, or a dropped inconvenient result, stop. That is not adaptation.
2. Confirm the journal and article type. Read the current Aims and Scope and Instructions for Authors on the journal site, for the exact article type: original research, review, case report, short communication, methods paper, or another type the journal lists. Record the article type you are claiming and why the work qualifies for it. A case series filed as original research, or a narrative review filed as systematic, fails at screening. If the type is unclear, use a presubmission inquiry where the journal offers one. See references/presubmission-inquiry-and-cover-letter.md.
3. Study recent papers in the journal. Pick 8 to 12 papers from the last two years in the same article type, favouring papers close in topic or method. Do not study editorials or papers in a different type. For each one record title pattern, abstract form and length, section order, main text length, number of tables and figures, reference count and age mix, how the introduction ends, and how the discussion opens. Use assets/journal-profile.md and the method in references/journal-study-method.md. One paper is an anecdote. The pattern across 8 to 12 is the journal.
4. Build the journal profile. Fill one profile per target journal: scope wording in the journal own terms, readership, article type rules, hard limits for main text, abstract, references, tables and figures, required sections and their order, structured or unstructured abstract and its headings, citation style and reference formatting, reporting guideline required for the design, ethics, funding, conflict, data availability and author contribution statements required, file and figure specs, and any journal specific extras such as key points, highlights, graphical abstract, or plain language summary. Pull every limit from the current author guidelines. Never carry limits over from a previous journal.
5. Map the gap, section by section. Compare the draft to the profile in references/adaptation-map.md. For each section write current state, target state, and the exact edit. Sort edits into three buckets: framing edits (title, abstract, keywords, introduction opening and closing, discussion opening, cover letter), structure edits (section order, headings, moving material to supplement, splitting or merging sections), and compliance edits (length cuts, reference style, statements, checklists, figure files). Framing first, structure second, compliance last. Polish only after the science and the fit are settled.
6. Cut or expand to length by moving, not by hollowing out. If the draft is over the limit, first move methods detail, extra tables, and secondary analyses to a supplement where the journal allows one, then cut background that the journal readership already knows, then tighten prose. Never cut methods detail that a reader needs to judge or repeat the work, and never cut a result to save words. If the draft is well under the limit, do not pad. A short paper inside the limit is fine. Add only material the journal papers normally include and the work actually has, such as a limitations paragraph or a clearer contribution statement.
7. Rewrite the front door: title, abstract, keywords. Match the title pattern the journal study found: descriptive or declarative, whether a design label is included, and typical length. Rewrite the abstract to the journal form: if structured, use its exact headings and cover background, methods, results with numbers, and conclusion in that order. Keep every number identical to the findings lock. Pick keywords the journal indexing expects, including a controlled vocabulary term where the journal asks for one, rather than repeating title words only.
8. Reframe the introduction and discussion for this readership. In the introduction, cite the conversation this journal has actually been having: include relevant recent papers from the target journal where they genuinely belong, engage them on substance, and end with the gap and contribution stated in terms that readership cares about. Never add a citation to a journal paper that is not relevant just to signal fit. In the discussion, open the way the studied papers open, usually with the main finding in plain terms, then place the result against prior work, then limits, then implications for the audience this journal serves. The findings do not change. The neighbours, emphasis, and implications do.
9. Fix citations and reporting to the journal rules. Convert references to the journal citation style, check every reference against the source it claims to support, and complete the reporting checklist for the design where one applies. Common pairings listed by the EQUATOR Network include CONSORT for randomised trials, STROBE for observational studies, PRISMA for systematic reviews, STARD for diagnostic accuracy, CARE for case reports, and ARRIVE for animal studies. Use the current checklist from EQUATOR, not a copy remembered from a prior paper. Complete required statements even when the answer is none, no funding, or not applicable, in the wording the journal asks for.
10. Write a fresh cover letter for this journal. One page. State the article type, the question and main finding in two or three sentences, why this journal readership is the right audience stated with a specific scope link, what is new against work the journal has published, and the required declarations: not under consideration elsewhere, all authors approve, ethics and conflicts as applicable. Rewrite it for every new target. A cover letter that names the wrong journal or describes a different paper is an instant credibility loss. Template in references/presubmission-inquiry-and-cover-letter.md.
11. Run the fit check. Fill assets/fit-check.md, then run python3 bin/fit_check.py --profile profile.json --manuscript manuscript.txt for the countable parts: main text words, abstract words, reference count, and required section presence. Fix every hard fail: over a hard limit, missing required section, missing required statement, wrong article type. Score the judgement parts honestly: scope fit, framing fit, citation fit. If scope scores low, the right move is a different journal, not harder rewriting. See the worked example in references/worked-example.md.
12. Do a final integrity pass. Diff the adapted draft against the findings lock: every number, direction, and claim should match. Confirm no result was dropped, no claim grew, no limitation vanished in the cuts. Confirm author list, affiliations, and corresponding author details match the journal title page rule. Then submit once, to this journal only.

Output Contract

• A findings lock, one page, that the adaptation never contradicts.
• A completed journal profile in assets/journal-profile.md form, sourced from the current author guidelines and from 8 to 12 recent papers in the same article type.
• An adaptation map with one row per section: current state, target state, exact edit, bucket, and status.
• The adapted manuscript, with title, abstract, and keywords rewritten to the journal form and all numbers unchanged from the findings lock.
• A fresh cover letter for this journal, or a presubmission inquiry if that step comes first.
• A fit check report: checker output with zero hard fails, plus scored judgement items, and a clear submit, fix, or change journal verdict.

Operating Rules

1. Verify every limit, section rule, and checklist requirement on the target journal site at the time of adaptation. Guidelines change. A remembered limit is a lead, not a fact. Unverifiable, flag it as unchecked rather than stating it.
2. Never change findings to fit a journal. No new numbers, no stronger claims, no dropped results, no softened limitations that change their meaning. Adaptation changes presentation, framing, order, length, and compliance only.
3. Never add a citation for fit alone. Cite a paper from the target journal only when it is relevant to the argument and has been read closely enough to describe accurately.
4. Submit to one journal at a time. Do not adapt the same manuscript for parallel submission, and disclose prior submission history where the new journal asks for it.
5. Match the article type to what was actually done. Do not relabel a narrative review as systematic, a case series as a trial, or a short report as a full article to reach a different limit set.
6. Keep length cuts honest. Moving material to a supplement the journal offers is fine. Cutting methods or results a reader needs is not, even if it gets the word count down.
7. Complete ethics, funding, conflict, data, and contribution statements truthfully, including when the answer is none. Never invent an approval number, a funder, or a registration.
8. Style: plain, direct, varied rhythm. No em dashes.