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lbcb-sci / racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads
MIT License
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Does racon_wrapper lack --no-trimming option #78

Open SalvadorGJ opened 1 year ago

SalvadorGJ commented 1 year ago

Hi,

I want to test racon_wrapper v1.5.0, with the following command:

racon_wrapper \\
        -t ${task.cpus} \\
        -u --no-trimming \\
        --split 16000000 \\
        ${fastq_file} ${sam_file} ${genome_file} 1> ${file_name}.racon_polished.fa

Unfortunately, this is the output error:

usage: racon_wrapper [-h] [--split SPLIT] [--subsample SUBSAMPLE SUBSAMPLE]
                     [-u] [-f] [-w WINDOW_LENGTH] [-q QUALITY_THRESHOLD]
                     [-e ERROR_THRESHOLD] [-m MATCH] [-x MISMATCH] [-g GAP]
                     [-t THREADS]
                     [--cudaaligner-band-width CUDAALIGNER_BAND_WIDTH]
                     [--cudaaligner-batches CUDAALIGNER_BATCHES]
                     [-c CUDAPOA_BATCHES] [-b]
                     sequences overlaps target_sequences
racon_wrapper: error: unrecognized arguments: --no-trimming

So I want to ask, is this the expected behaviour and I should not use the --no-trimming parameter?

Kind regards, Salvador