Critical Input Error: Fails to validate any input format for BAM files

[SooryaChandra]

Hello LAAVA developers,

I am trying to run the LAAVA pipeline on the public PacBio ssAAV dataset but am consistently running into an Invalid input parameters error at the very beginning of the run. The --help flag also fails with the same error, making it difficult to debug.

I have tried multiple input formats based on the error message and standard Nextflow conventions, but all have failed.

My Setup:

• Nextflow Version: 25.04.3
• Run Environment: Ubuntu (via WSL2) with Conda

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Attempt 1: Direct path to tagged BAM file

• Command: nextflow run formbio/laava -r main --bam_input data/AAV_Sample_1/m84026_231030_220704_s3.tagged.bam ...
• Result: Invalid input parameters.

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Attempt 2: TSV Sample Sheet pointing to a folder

• samplesheet.tsv contents:

  sample_id	sample_folder
  AAV_Sample_1	/home/bhanu/laava_analysis_run/data/AAV_Sample_1

• Command: nextflow run formbio/laava -r main --input samplesheet.tsv ...
• Result: Invalid input parameters.

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Attempt 3: TSV Sample Sheet pointing to a raw HiFi BAM file

• samplesheet.tsv contents:

  sample_id	hifi_reads
  AAV_Sample_1	/home/bhanu/laava_analysis_run/data/m84026_231030_220704_s3.hifi_reads.bam

• Command: nextflow run formbio/laava -r main --input samplesheet.tsv --aav_reference ...
• Result: Invalid input parameters.

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Could you please provide working command and sample sheet format for running the pipeline on a single PacBio HiFi BAM file (either raw hifi_reads.bam or a pre-aligned tagged.bam)?

Thank you for your time and for developing this tool.