docs: Apps updates — authoring, execution, and workflow docs#20
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Update the apps and jobs workflow to describe the current launch form tabs: resources are configured from the Cluster tab's Resources section, not a top-level Resources tab. Co-authored-by: Codex <codex@openai.com>
Sweep of accuracy fixes flagged in the apps code review: - #21 Replace the removed "Pull latest" tip with guidance to use Update before launching. - #23 Fix the "Delete" vs "Remove" wording and the garbled remove-app sentence; the UI uses "Remove". - #24 Document the env_parameters runnable field (Environment tab). - #25 Requirement check runs at job runtime after PATH/conda/env setup but before pre_run and the main command — not "prepended at submission time". Show it in the correct position in the example script. - #26 Auto-detection is a repository-root-only fallback used only when no runnables.yaml exists anywhere; Pixi task env vars map to the runnable's env defaults (not "--env:" flags); Pixi apps are named repo/branch in a Git clone. - #27 Remove the non-existent admin container-cache override; only a per-user Preferences override exists. - #28 Add a "Using the App Catalog" section covering browse, add, share, unshare, and listing behavior. 🤖 Generated with [Claude Code](https://claude.com/claude-code)
Update the auto-detection reference to match the generated command `cd "$FG_WORK_DIR" && nextflow run repo -ansi-log false`, and explain that running from the work dir keeps .nextflow.log, .nextflow/, and work/ out of the shared repo cache. 🤖 Generated with [Claude Code](https://claude.com/claude-code)
Add working_dir to the manifest field table, a "Working Directory" section in the execution guide (repo vs work, and why containers default to work), and update the Nextflow auto-detection reference to the clean `nextflow run repo` + working_dir: work form. 🤖 Generated with [Claude Code](https://claude.com/claude-code)
Update the Apps documentation to match the current implementation, including the recent revision-pinning work and the App Catalog sharing feature. User guide (workflows/apps-and-jobs): - Rename the Add App "branch" field to "Revision" (tag or branch) and explain that the revision is fixed/pinned when an app is added. - Document the App Catalog: My Apps / App Catalog / Jobs tabs, sharing to the catalog with name/description overrides, adding shared apps, and unsharing. - Fix the launch-form "Resources" tab to its actual name, "Cluster". - Correct the submit button label to "Submit Job" / "Start Service". - Remove the nonexistent "Pull latest" toggle; point to the Update action. - Add the Job Detail "Overview" tab; clarify what Update does under pinning. - Fix a typo in Removing an App. Authoring guide: - Manifest discovery: describe the actual two-pass behavior (walk for runnables.yaml anywhere; only if none exists do adapters run, at the repo root only) instead of a per-directory precedence order. - Nextflow auto-detection command is "nextflow run repo -ansi-log false", run from the work dir (not "nextflow run ."). - Pixi auto-detection exports task env vars as the runnable's default env vars, not as removed "--env:VARNAME" hidden parameters. - Document the runnable "working_dir" field. - Clarify that the requirement check runs after env setup but before pre_run/command, not "at submission time". Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Brings the Apps documentation in line with current functionality, consolidating the
apps-updateswork with the recent sync pass fromdocs/apps-sync-recent-changes.Highlights
User guide (
workflows/apps-and-jobs)Authoring guide
runnables.yamlanywhere; auto-detection only at the repo root, only when none exists).nextflow run repo -ansi-log falsefrom the work dir.working_dirfield and a dedicated Working Directory section in the execution guide.pre_run/command.🤖 Generated with Claude Code