paperpush: Skill for Claude Code

.claude/skills/paperpush-prepare-submission/SKILL.md

paperpush-prepare-submission is a skill for Claude Code from pachterlab/paperpush. It costs 100 tokens per session (1,220 once invoked), scanned A, original, BSD-2-Clause.

A workflow for preparing and submitting a research manuscript from a directory of files. It resolves or creates the venue's .sub submission file, fills and validates it, then logs in and submits it after the user approves.

In plain words
What is it for?
Use it when you want to prepare or submit a manuscript to a supported venue. Provide the manuscript directory and, if needed, the venue; the workflow can use an existing .sub file or create one.
Why use it?
It brings separate preparation, validation, login, and submission steps into one process and reduces manual handling of the submission file.

Skill for Claude Code

Written for Claude Code: installed under .claude/.

This is pachterlab/paperpush's own configuration. It tells Claude Code how to work on paperpush itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything paperpush configures →

Reuse

Borrowing it

Nothing to install: this file belongs to pachterlab/paperpush. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/pachterlab/paperpush/main/.claude/skills/paperpush-prepare-submission/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/pachterlab/paperpush

Made for: Claude Code.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

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README.md
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Your own site · 80×15
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Per session 100 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,220 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00100 $0.01220
Opus 5 $0.00050 $0.00610
Sonnet 5 $0.00020 $0.00244
Haiku 4.5 $0.00010 $0.00122

Measured 10d ago against content hash 431c46398e68, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-09, from the pricing page.

Security

Grade A, and why

paperpush-prepare-submission scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 10d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

.claude/skills/paperpush-prepare-submission/SKILL.md · 116 lines

How it starts

The opening of the file, as written. The whole thing — 116 lines — stays where its author put it; the contents beside it link to each section on GitHub.

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
      

Read the full file on GitHub · 116 lines

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 10d ago First seen · 116 lines · 100 tokens per session scan A 431c46398e68

Subscribe to this mod's changes

paperpush-prepare-submission is a skill published in the GitHub repository pachterlab/paperpush (164 stars, last pushed 8d ago), licensed BSD-2-Clause. It adds 100 tokens to every session and 1,220 once invoked, about $0.0005 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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