Closed ctr26 closed 4 years ago
Hi @ctr26 - as nanopolish requires signal level data, you'll need to provide fast5 files to run the --nanopolish
pipeline. The --medaka
pipeline doesn't have this requirement so should work just fine with just fastq files. This is documented in the --help
, but it seems I've missed documenting it somewhere else so please point me to where I've missed this so that I can correct it!
"Use --nanopolish or --medaka to run these workflows. --basecalled_fastq should point to a directory created by guppy_basecaller (if you ran with no barcodes), or guppy_barcoder (if you ran with barcodes). It is imperative that the following guppy_barcoder command be used for demultiplexing:"
From the readme it doesn't explicitly state this
nextflow run main.nf -profile docker --nanopolish --prefix "ena" --fast5_pass ...
nanopolish will run with a empty fast5_pass directory (would be good if it returned an error and asked if the user wanted to use medaka instead)
I should've read the help carefully though because it is quite obvious and I'm not sure how I missed it :
"--fast5_pass Directory containing fast5 files - usually fast5_pass. NOT REQUIRED FOR MEDAKA WORKFLOW."
I have for fastq.gz files that have been:
But they don't come with fast5 files. If I don't provided a "--fast5-directory" directory then the pipeline fails at "articMinIONNanopolish" as it tries to name a folder as "false". Are the fast5 files not as optional the help guide claims?
Best
Craig