Guppy
Guppy
- description
- Run Guppy basecaller on ONT FAST5 files. The docker tag number will match the version of Guppy that is being run. You can change this value to run a different version of Guppy. Currently supports... [3.5.2, 3.6.0, 4.0.14]. All fast5 files within the given GCS dir, gcs_fast5_dir, will be processed. Takes a few hours to process 130GB. Best guess is that the processing time scales linearly but untested.
Inputs
Required
config
(String, required): Guppy config file.gcs_fast5_dir
(String, required): GCS path to a directory containing ONT FAST5 files.gcs_out_root_dir
(String, required): GCS path to a directory where the output will be written.
Optional
barcode_kit
(String?): Optional. Barcode kit used for sequencing.num_shards
(Int?): Optional. Number of shards to use for parallelization. Default is 1 + ceil(length(read_lines(ListFast5s.manifest))/100).protocol_run_id
(String?): Optional. Protocol run ID used for sequencing. Default is 'unknown'.sample_name
(String?): Optional. Sample name used for sequencing. Default is 'unknown'.Basecall.runtime_attr_override
(RuntimeAttr?)FinalizeBasecalls.runtime_attr_override
(RuntimeAttr?)ListFast5s.runtime_attr_override
(RuntimeAttr?)MakeFinalSummary.runtime_attr_override
(RuntimeAttr?)MakeSequencingSummary.runtime_attr_override
(RuntimeAttr?)PartitionFast5Manifest.runtime_attr_override
(RuntimeAttr?)SumFailingFastqs.runtime_attr_override
(RuntimeAttr?)SumPassingFastqs.runtime_attr_override
(RuntimeAttr?)TimestampStopped.runtime_attr_override
(RuntimeAttr?)UniqueBarcodes.runtime_attr_override
(RuntimeAttr?)
Defaults
flow_cell_id
(String, default="unknown"): Optional. Flow cell ID used for sequencing. Default is 'unknown'.instrument
(String, default="unknown"): Optional. Instrument used for sequencing. Default is 'unknown'.SumFailingFastqs.prefix
(String, default="sum")SumPassingFastqs.prefix
(String, default="sum")
Outputs
gcs_dir
(String)barcodes
(Array[String])num_fast5s
(Int)num_pass_fastqs
(Int)num_fail_fastqs
(Int)