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Agent skill

Paperpush Prepare Submission

by pachterlab in pachterlab/paperpush

End-to-end paperpush submission flow from a manuscript directory: resolve the .sub (user-provided, else an existing one in the manuscript directory, else created on the fly), autofill it, validate…

BSD-2-ClauseAuto-check passed

Install Paperpush Prepare Submission

skills CLI
$ npx skills add pachterlab/paperpush --skill paperpush-prepare-submission -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install pachterlab/paperpush paperpush-prepare-submission --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/pachterlab/paperpush.git skills-src && mkdir -p .claude/skills && cp -r skills-src/.claude/skills/paperpush-prepare-submission .claude/skills/paperpush-prepare-submission && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
paperpush-prepare-submission
GitHub stars
206
Token cost
~1.2k tokens
SKILL.md length
656 words
Files
1
Skills in repo
2
Repo updated
First seen
Licence
BSD-2-Clause

At a glance

End-to-end paperpush submission flow from a manuscript directory: resolve the .sub (user-provided, else an existing one in the manuscript directory, else created on the fly), autofill it, validate…

  • Works in 2 steps: The manuscript directory — required. If… → The venue slug (e.g. bioinformatics). If…
  • A general prepare/submit my manuscript request
  • SKILL.md covers Inputs you need, Steps and Rules
  • Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md

What it does

Paperpush Prepare Submission is an agent skill from pachterlab/paperpush. End-to-end paperpush submission flow from a manuscript directory: resolve the .sub (user-provided, else an existing one in the manuscript directory, else created on the fly), autofill it, validate, then log in and submit. Use for a general "prepare/submit my manuscript" request. Triggers: "prepare my manuscript for submission to <venue", "submit my manuscript to <venue", "get my paper ready to submit with paperpush".

Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.

The repository describes itself as: 📝 Automated manuscript validation and submission portal completion. The licence is BSD-2-Clause.

When your agent uses it

  • A general prepare/submit my manuscript request

Example prompts

  • “prepare/submit my manuscript”
  • “prepare my manuscript for submission to <venue”
  • “submit my manuscript to <venue”
  • “/paperpush-prepare-submission”

Workflow steps

2 steps, taken from the first numbered list in SKILL.md.

  1. The manuscript directory — required. If the user did not give it, ask in
  2. The venue slug (e.g. bioinformatics). If the user did not say it, ask

What it can do on your machine

Read from SKILL.md and the folder at commit 34b250c. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    No scripts in the folder and no shell commands in SKILL.md.

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    No URLs in SKILL.md.

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Paperpush Prepare Submission loads about 1.2k tokens when it runs. Until then it costs about 113 tokens; SKILL.md has 656 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~113
When it runs · the whole SKILL.md, loaded when a task matches
~1.2k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.

SKILL.md

The full file from pachterlab/paperpush at commit 34b250c, republished under its BSD-2-Clause licence (© pachterlab). 656 words, ~1,226 tokens.

Download SKILL.mdSave it as .claude/skills/paperpush-prepare-submission/SKILL.md (or your agent's skills folder).
name
paperpush-prepare-submission
description
End-to-end paperpush submission flow from a manuscript directory: resolve the .sub (user-provided, else an existing one in the manuscript directory, else created on the fly), autofill it, validate, then log in and submit. Use for a general "prepare/submit my manuscript" request. Triggers: "prepare my manuscript for submission to <venue>", "submit my manuscript to <venue>", "get my paper ready to submit with paperpush".

paperpush prepare & submit (Claude skill)

Orchestrates the full submission path for a manuscript directory when the user has not named a .sub file. It generates the .sub, hands off to the paperpush-autofill skill to fill it, validates, and then (with the user's go-ahead) logs in and submits. This skill only sequences the steps; each underlying paperpush command does the real work.

Inputs you need

  1. The manuscript directory — required. If the user did not give it, ask in plain text (a path is free-text; do not use a multiple-choice prompt). Never guess it, scan the repository for candidate folders, or fall back to test fixtures.
  2. The venue slug (e.g. bioinformatics). If the user did not say it, ask or infer it from their message. Confirm it is supported with paperpush --venues.

Do not ask for a .sub path. Resolve it by this hierarchy: (1) an explicit .sub the user provided; (2) else an existing <venue>.sub in the manuscript directory; (3) else create <venue>.sub in the manuscript directory on the fly. See step 1.

Steps

  1. Check the login first, before any other work. Run:

    paperpush login --list

    If the venue is not listed (or the output is Not logged in to any venues.), tell the user immediately — in your next message, not at the end — to run

    paperpush login <venue>

    themselves in a terminal, since it opens a browser and may need their password, ORCID, CAPTCHA, or two-factor code. Then carry on with steps 1-3 anyway while they do it; a missing login only blocks step 5.

  2. Resolve the .sub by hierarchy (user-provided > in manuscript dir > create on the fly):

    • If the user named a .sub path, use it as-is.

    • Else if <manuscript-dir>/<venue>.sub already exists, reuse it (do not overwrite unless the user asks to regenerate).

    • Else create it in the manuscript directory, with an absolute path:

      paperpush subfile <venue> --fill-defaults -o <manuscript-dir>/<venue>.sub

    A newly created .sub lives alongside the manuscript. Use the resolved path for every later step.

  3. Autofill the .sub. Invoke the paperpush-autofill skill (via the Skill tool), passing the .sub path from step 1 and the manuscript directory. That skill reads the files, extracts field values, and applies them through paperpush autofill. Let it run to completion and relay its summary of what was filled and what it left for the user.

  4. Validate. Run the pre-submission checks:

    paperpush validate <resolved-sub-path>

    If validation reports errors, stop here. Report the exact errors and the review-flagged / never fields the autofill skill left for the user, and do not proceed to login or submit until they are resolved. A file with validation errors will not submit.

  5. Confirm the login landed. Re-run paperpush login --list (or paperpush login <venue> --status). If the venue is now listed, go on to step 5. If it still is not, stop and wait — repeat the step-0 ask that the user run paperpush login <venue> in their terminal. Logging in opens a browser and may require their password, ORCID, CAPTCHA, or two-factor prompt, so it is theirs to drive; do not run it for them.

  6. Submit (only after the user confirms). Submitting is outward-facing. Confirm explicitly first, then run:

    paperpush submit <resolved-sub-path>

    This opens a headed browser and walks the portal wizard, stopping before the final click so the user reviews everything in the submission system. Make clear that the final submit is theirs to click.

Show full SKILL.md (103 more words)Show less

Rules

  • Always use absolute paths for the .sub file and the manuscript directory.
  • Never infer the manuscript directory; ask (in plain text) if it is missing.
  • Generate the .sub in the manuscript directory, not the working directory.
  • Check paperpush login --list up front and surface a missing login immediately, so the user can log in while you do the rest of the work.
  • Never run paperpush login yourself — it is interactive and belongs in the user's terminal.
  • Do not run submit without explicit user confirmation, and never past a failed validate.
  • Delegate all field extraction to paperpush-autofill; do not duplicate its logic here.

© pachterlab, BSD-2-Clause. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

Just SKILL.md in .claude/skills/paperpush-prepare-submission of pachterlab/paperpush.

Open the folder on GitHubat commit 34b250c

Compare with similar skills

Paperpush Prepare Submission next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Paperpush Prepare Submission compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Paperpush Prepare Submission this skillpachterlab/paperpush206—~1.2kAutomated safety check: PassBSD-2-Clause
Release PreparationCherryHQ/cherry-studio53k—~4.3kAutomated safety check: PassAGPL-3.0
Audit Preparationsickn33/agentic-awesome-skills47k1 repos~5.3kAutomated safety check: PassMIT
Directory Submissionscoreyhaines31/marketingskills54k2 repos~6.7kAutomated safety check: PassMIT
Prepare Paperclip PRpaperclipai/paperclip100k—~954Automated safety check: PassMIT
Prepare MCP Integrationpaperclipai/paperclip100k—~3.1kAutomated safety check: PassMIT

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Questions about Paperpush Prepare Submission

What does Paperpush Prepare Submission do?

End-to-end paperpush submission flow from a manuscript directory: resolve the .sub (user-provided, else an existing one in the manuscript directory, else created on the fly), autofill it, validate…. Paperpush Prepare Submission is an agent skill from pachterlab/paperpush.sub (user-provided, else an existing one in the manuscript directory, else created on the fly), autofill it, validate, then log in and submit.

When should I use Paperpush Prepare Submission?

Paperpush Prepare Submission fits situations like: A general prepare/submit my manuscript request.

How do I install Paperpush Prepare Submission in Claude Code?

Run `npx skills add pachterlab/paperpush --skill paperpush-prepare-submission -a claude-code`. Or copy the skill folder (.claude/skills/paperpush-prepare-submission in pachterlab/paperpush) into .claude/skills/paperpush-prepare-submission in your project. Claude Code loads it when a task matches its description.

How do I install Paperpush Prepare Submission in Codex?

Run `npx skills add pachterlab/paperpush --skill paperpush-prepare-submission -a codex`. Or copy the skill folder (.claude/skills/paperpush-prepare-submission in pachterlab/paperpush) into .agents/skills/paperpush-prepare-submission in your project. Codex loads it when a task matches its description.

Can I use Paperpush Prepare Submission in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add pachterlab/paperpush --skill paperpush-prepare-submission -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/paperpush-prepare-submission, .gemini/skills/paperpush-prepare-submission, .github/skills/paperpush-prepare-submission and .opencode/skills/paperpush-prepare-submission in your project.

What does Paperpush Prepare Submission need to run?

SKILL.md names no scripts, command-line tools or credentials: Paperpush Prepare Submission is instructions for the agent only.

Does Paperpush Prepare Submission access the network?

SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.

Is Paperpush Prepare Submission safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.

What licence does Paperpush Prepare Submission use?

Paperpush Prepare Submission is published under the BSD-2-Clause licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Paperpush Prepare Submission use?

About 1.2k tokens (SKILL.md is roughly 4.9k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.

What are the alternatives to Paperpush Prepare Submission?

Skills that share tags, products or a category with Paperpush Prepare Submission: Release Preparation (CherryHQ/cherry-studio, 53k stars), Audit Preparation (sickn33/agentic-awesome-skills, 47k stars), Directory Submissions (coreyhaines31/marketingskills, 54k stars) and Prepare Paperclip PR (paperclipai/paperclip, 100k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Paperpush Prepare Submission?

pachterlab (a GitHub organization) maintains it in pachterlab/paperpush, which has 206 GitHub stars. The repository holds 2 skills in this directory. The repository was last updated on October 2, 2026.

Source: pachterlab/paperpush on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.