Run the nf-core/lsmquant pipeline for light-sheet microscopy image preprocessing and analysis.
npx skills add https://github.com/danilomonge/nf-claw --skill lsmquant
Please help me install this Agent Skill. Skill: lsmquant Source: https://github.com/danilomonge/nf-claw/tree/main/pipelines/lsmquant Command: npx skills add https://github.com/danilomonge/nf-claw --skill lsmquant
It helps researchers run the nf-core/lsmquant workflow without guessing flags, manually checking schema files, or drifting from the pinned release.
Use the lsmquant skill to run the pinned pipeline on your samplesheet and save the results to your chosen output directory.
High-intent search queries and answers about installing and using this skill.
Run the nf-core/lsmquant pipeline by providing a valid input samplesheet CSV, an output directory, and schema-constrained parameters to execute preprocessing, stitching, alignment, registration, and nuclei quantification for tissue-clearing imaging workflows.
Light-sheet microscopy image analysis requires a valid input CSV samplesheet, an output directory, and schema-constrained parameters aligned with the pinned pipeline release and Nextflow runtime to process tissue-clearing imaging data.
Yes, the pipeline applies to tissue-clearing imaging workflows that require staged stitching, alignment, registration, and nuclei quantification, starting from a standardized samplesheet input.
Schema validation checks parameters against the pinned pipeline release schema, ensuring invalid values fail fast before execution. This prevents parameter drift and enforces reproducible bioinformatics analysis runs.
Use a pinned pipeline release bundled in the repository with schema-backed options and validated inputs. This produces module results, pipeline info, and run logs suitable for repeatable bioinformatics analysis.
Yes, the pipeline requires the Nextflow runtime and schema-constrained parameters aligned with the pinned pipeline release to execute light-sheet microscopy preprocessing and nuclei quantification workflows.
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