CLI Parameters

Command Line Arguments Summary

Below is a breakdown of all relevant nimble commands and their CLI arguments.

generate

Generates a reference library.

Flag	Long Name	Description	Required?	Takes Value
--file	--file	Input FASTA or CSV file	✅	✅
--opt-file	--opt-file	Optional CSV file with metadata	❌	✅
--output_path	--output_path	Output JSON file	✅	✅

Example Usage:

python -m nimble generate --file reference.fasta --output_path library.json

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align

Aligns input RNA-seq or scRNA-seq data to the reference library.

Flag	Long Name	Description	Required?	Takes Value
-r	--reference	Reference library file(s) (.json)	✅	✅
-o	--output	Output TSV file(s)	✅	✅
-i	--input	Input sequencing file(s) (.fastq, .fastq.gz, or .bam)	✅	✅
-c	--cores	Number of CPU cores for alignment (default: 1)	❌	✅
-f	--strand_filter	Strandedness filtering (unstranded, fiveprime, threeprime, none) (default: unstranded)	❌	✅
-t	--trim	Read trimming configuration (<TARGET_LENGTH>:<STRICTNESS>)	❌	✅
-p	--force_bam_paired	Force paired-end alignment for BAM files	❌	❌

Example Usage:

python -m nimble align -r library.json -i input.fastq.gz -o results.tsv

Note: you can align more than one library at a time -- each -r should correspond to each -o.

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report

Generates a summarized feature-by-cell matrix from alignment results.

Flag	Long Name	Description	Required?	Takes Value
-i	--input	Input alignment results file (.tsv)	✅	✅
-o	--output	Output summary file (.tsv)	✅	✅
-t	--threshold	Proportional count threshold for filtering features (default: 0.05)	❌	✅
	--disable_thresholding	Disable per-UMI thresholding	❌	❌

Example Usage:

python -m nimble report -i results.tsv -o summary.tsv

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download

Downloads the latest or a specific version of the aligner.

Flag	Long Name	Description	Required?	Takes Value
--release	--release	Specify a release version	❌	✅

Example Usage:

python -m nimble download --release v0.0.1

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plot

Generates an HTML report from nimble output.

Flag	Long Name	Description	Required?	Takes Value
--input_file	--input_file	Input nimble counts file	✅	✅
--output_file	--output_file	Output HTML report	✅	✅

Example Usage:

python -m nimble plot --input_file summary.tsv --output_file report.html