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Version 6.0.4 bump
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minknowbot committed Jul 31, 2024
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4 changes: 2 additions & 2 deletions dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
cryptography~=39.0
grpcio==1.41.0
grpcio-tools==1.41.0
grpcio==1.60.0
grpcio-tools==1.60.0
minknow-api-service-plugin
pre-commit
pytest
12 changes: 12 additions & 0 deletions proto/minknow_api/acquisition.proto
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Expand Up @@ -665,6 +665,9 @@ message AcquisitionConfigSummary {
bool basecalling_enabled = 1;
// Basecalling configuration filename (if basecalling enabled)
string basecalling_config_filename = 16;
// Basecalling model version (empty if basecalling not enabled)
// Since 6.0
string basecalling_model_version = 24;
// Was the experiment a duplex basecalling experiment (false if basecalling is disabled)
bool duplex_enabled = 23;

Expand All @@ -682,8 +685,12 @@ message AcquisitionConfigSummary {


// Is lamp enabled for the run
//
// DEPRECATED 6.0: Lamp support has been removed and this value will always be false.
bool lamp_enabled = 15;
// The LAMP kit used (if LAMP enabled)
//
// DEPRECATED 6.0: Lamp support has been removed and this value will always be empty.
string lamp_kit = 20;

// Root directory reads were written to for the run.
Expand Down Expand Up @@ -878,6 +885,11 @@ message AcquisitionRunInfo {
// describing the current finishing state.
FinishingState finishing_state = 10;

// Progress through the current finishing state, ranges from 0 - 1.
//
// This will increase from 0 -> 1 for each individual finishing state, then reset.
float finishing_state_percent_complete = 17;

// The reason the acquisition period was ended.
AcquisitionStopReason stop_reason = 3;

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106 changes: 66 additions & 40 deletions proto/minknow_api/analysis_configuration.proto
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Original file line number Diff line number Diff line change
Expand Up @@ -311,6 +311,12 @@ message ReadFilters {
// If set to zero (the default), this test is not applied (as though it had been set to a value
// longer than any possible read).
uint32 event_count_max = 4;

// Control whether reads unblocked using from `DataService::get_live_reads()` should be filtered.
//
// When set to true, reads which are unblocked by `get_live_reads` are filtered and therefore not basecalled.
// When set to false, reads that are unblocked by `get_live_reads` will not be filtered and therefore will be basecalled.
bool skip_rejected_reads = 5;
}

message ReadClassificationParams {
Expand Down Expand Up @@ -406,6 +412,25 @@ message ReadClassificationParams {
// for other classification strategies.
//
google.protobuf.UInt32Value selected_classifications_chunks_required = 10;

// this parameter controls whether (or not) we merge data for all selected classifications into a single
// data point before deciding whether to output a read.
// For instance, if 2 classifications are selected and classification A is 20% of the read, and classification B
// is 20% of the read then:
// When merge_selected_classifications is set to true, the overall selected classification proportion would amount
// to 40% of the read and that value would used when deciding whether or not to output the read.
// When merge_selected_classifications is set to false, each selected classification would be considered
// separately at the decision stage. Defaults to false.
// Note that when multiple classifications are selected by the user and the threshold criteria are met, then the
// most recent classification (of all selected classifications) will be used as the read overall classification.
//
google.protobuf.BoolValue merge_selected_classifications = 11;

// Limit on how long a read may be in seconds before minknow forces the selected decision and either
// selects or vetoes the complete read.
//
// If unspecified a default value is used.
google.protobuf.UInt64Value max_read_length_before_selected_decision_seconds = 12;
}

message ChannelStates {
Expand Down Expand Up @@ -670,7 +695,7 @@ message BarcodingConfiguration
// If no barcoding kits are supplied, barcoding is disabled.
repeated string barcoding_kits = 1;

// Whether Guppy should trim barcodes
// Whether the basecaller should trim barcodes
// If not specified, this value defaults to false (not triming barcodes)
// If barcoding is not enabled (e.g., because no barcoding kits are specified),
// this parameter has no effect.
Expand All @@ -679,31 +704,18 @@ message BarcodingConfiguration
// Barcode is only classified if a barcode above `min_score` is present at both ends of the basecalled read.
bool require_barcodes_both_ends = 3;

// Search for barcodes through the entire length of the read.
//
// If a barcode is found in the middle of a read the read is marked as unclassified.
bool detect_mid_strand_barcodes = 4;

// Minimum alignment score to consider a valid barcode.
//
// Maximum value is 100, defaults to 60.
google.protobuf.FloatValue min_score = 5;

// Minimum score to consider a valid barcode (overrides min_score for rear barcodes).
//
// Maximum value is 100, defaults to min_score if not specified.
google.protobuf.FloatValue min_score_rear = 6;

// Minimum score to consider a valid mid barcode (only valid if detect_mid_strand_barcodes is specified).
//
// Maximum value is 100, defaults to 60.
google.protobuf.FloatValue min_score_mid = 7;

// The minimum score required for the barcode mask to be detected.
//
// Maximum value is 100, defaults to 40.
google.protobuf.FloatValue min_score_mask = 8;

reserved "detect_mid_strand_barcodes";
reserved 4;
reserved "min_score";
reserved 5;
reserved "min_score_rear";
reserved 6;
reserved "min_score_mid";
reserved 7;
reserved "min_score_mask";
reserved 8;

// If set, barcodes that aren't in barcode user data list will be ignored
//
// Since 5.6
Expand All @@ -716,7 +728,7 @@ message AlignmentConfiguration
{
// Provide an index to align reads against once basecalled.
//
// Any acceptable reference format to guppy can be passed here:
// Any acceptable reference format to the basecaller can be passed here:
// - fasta reference file
// - minimap index file
repeated string reference_files = 1;
Expand All @@ -726,7 +738,7 @@ message AlignmentConfiguration
// Note: alignment_index must be provided for this argument to be valid.
string bed_file = 2;

// Minimum coverage for guppy to accept an alignment.
// Minimum coverage for the basecaller to accept an alignment.
//
// If not specified a default value is used.
//
Expand All @@ -748,6 +760,8 @@ message AlignmentConfiguration
}

// Since 4.1
//
// DEPRECATED 6.0: Lamp support has been removed and all of these options will be ignored.
message LampConfiguration
{
// Set the lamp kit being used.
Expand Down Expand Up @@ -785,15 +799,15 @@ message BasecallerConfiguration
google.protobuf.UInt64Value max_bases = 3;
}

// Choose if guppy is enabled or disabled.
// Choose if the basecaller is enabled or disabled.
//
// If set to false then no basecalling will take place, and the rest of the config is ignored.
bool enable = 2;

// The Guppy cfg file with all the settings.
// The basecaller cfg file with all the settings.
//
// Filename can be absolute, or a basename (eg dna_r9.4_450bps.cfg)
// which guppy should locate (see guppy application config entry: "data_path")
// which the basecaller should locate (see basecaller application config entry: "data_path")
string config_filename = 1;

// Enable or disable pass/fail filtering based on alignment. When enabled, reads which
Expand Down Expand Up @@ -848,17 +862,19 @@ message BasecallerConfiguration
// If no configuration is specified lamp is disabled.
//
// Since 4.1
//
// DEPRECATED 6.0: Lamp support has been removed and this option will be ignored.
LampConfiguration lamp_configuration = 7;

// Enable read splitting in guppy.
// Enable read splitting in the basecaller.
//
// Since 4.5
//
// Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding when read splitting should be enabled.
bool enable_read_splitting = 8;

// Override score to use for guppy read splitting. If not specified a default value
// is used from guppy.
// Override score to use for the basecaller read splitting. If not specified a default value
// is used from the basecaller.
//
// Since 4.5
//
Expand All @@ -873,7 +889,13 @@ message SetBasecallerConfigurationRequest

message SetBasecallerConfigurationResponse{}

message GetBasecallerConfigurationRequest{}
message GetBasecallerConfigurationRequest
{
// The unique identifier assigned to this acquisition run.
//
// Since 6.0
string run_id = 1;
}

message GetPoreTypeConfigurationRequest {}

Expand Down Expand Up @@ -940,7 +962,6 @@ message SetPoreTypeConfigurationResponse {}
// - read_classification: The classification applied to the completed read (eg. strand).
// - batch_number: The batch number of this read, evaluated based on the destination file.
// - read_id: Unique read id for each read, formatted as a hash.
// - read_number: The read number (unique per channel, incrementing number assigned to each read by MinKNOW).
// - channel_name: The name of the channel which produced the read.
// - read_start_time: Read start time formatted in rfc3339 format.
// - basecall_status: Basecalling output status (derived from WriterDefaults section in analysis config).
Expand Down Expand Up @@ -1026,12 +1047,12 @@ message WriterConfiguration {
// Stored under /Analyses/Basecall_1D_*/BaseCalled_(template|complement)/Fastq
ChannelConfiguration fastq = 3;

// Trace table received from Guppy
// Trace table received from the basecaller
//
// Stored under /Analyses/Basecall_1D_*/BaseCalled_template/Trace
ChannelConfiguration trace_table = 11;

// Move table received from Guppy
// Move table received from the basecaller
//
// Stored under /Analyses/Basecall_1D_*/BaseCalled_template/Move
ChannelConfiguration move_table = 12;
Expand Down Expand Up @@ -1059,7 +1080,7 @@ message WriterConfiguration {

// The pattern used to find a fastq header.
//
// default: {read_id} runid={run_id} read={read_number} ch={channel_name} start_time={read_start_time}
// default: {read_id} runid={run_id} ch={channel_name} start_time={read_start_time}
// Where each {xxx} section is replaced with an attribute from the minknow state
// when the fastq is generated.
string fastq_header_pattern = 9;
Expand Down Expand Up @@ -1108,7 +1129,7 @@ message WriterConfiguration {

// The pattern used to find a fastq header.
//
// default: {read_id} runid={run_id} read={read_number} ch={channel_name} start_time={read_start_time}
// default: {read_id} runid={run_id} ch={channel_name} start_time={read_start_time}
// Where each {xxx} section is replaced with an attribute from the minknow state
// when the fastq is generated.
string header_pattern = 3;
Expand Down Expand Up @@ -1489,7 +1510,12 @@ message WriterConfiguration {
message SetWriterConfigurationResponse {
}

message GetWriterConfigurationRequest {
message GetWriterConfigurationRequest
{
// The unique identifier assigned to this acquisition run.
//
// Since 6.0
string run_id = 1;
}

message GetReadClassificationsRequest {}
Expand Down
38 changes: 38 additions & 0 deletions proto/minknow_api/analysis_workflows.proto
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Original file line number Diff line number Diff line change
@@ -0,0 +1,38 @@
syntax="proto3";

package minknow_api.analysis_workflows;

option java_package = "com.nanoporetech.minknow_api";
option objc_class_prefix = "MKAPI";

import "minknow_api/rpc_options.proto";

service AnalysisWorkflowsService {
rpc proxy (ProxyRequest) returns (stream ProxyResponse) {
option (experimental) = true;
}
}

message ProxyRequest {
// with parameters but without the endpoint e.g. for API /workflows/{id}/start:
// "/workflows/ae088129-8767-460f-8795-7c04771dc42f/start"
// "/workflows/epi2me-labs/wf-alignment/v1.2.8/start"
string api = 1;

enum Method {
GET = 0;
POST = 1;
PUT = 2;
DELETE = 3;
}

Method method = 2;

map<string, string> headers = 4;
string request_body = 3;
}

message ProxyResponse {
uint32 status_code = 1;
string response_body = 2;
}
19 changes: 16 additions & 3 deletions proto/minknow_api/basecaller.proto
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ option objc_class_prefix = "MKAPI";
import "google/protobuf/timestamp.proto";
import "google/protobuf/wrappers.proto";
import "minknow_api/analysis_configuration.proto";
import "minknow_api/analysis_workflows.proto";
import "minknow_api/protocol_settings.proto";
import "minknow_api/rpc_options.proto";

Expand Down Expand Up @@ -201,13 +202,13 @@ message StartBasecallingRequest {
// Options to control alignment performed once basecalling reads is complete.
analysis_configuration.AlignmentConfiguration alignment_configuration = 11;

// Enable read splitting in guppy
// Enable read splitting in the basecaller
//
// Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding when read splitting should be enabled.
bool enable_read_splitting = 13;

// Override score to use for guppy read splitting. If not specified a default value
// is used from guppy.
// Override score to use for the basecaller read splitting. If not specified a default value
// is used from the basecaller.
//
// Note: Since 5.9 this option has no effect, the basecaller is responsible for deciding when read splitting should be enabled.
google.protobuf.FloatValue min_score_read_splitting = 14;
Expand Down Expand Up @@ -235,6 +236,8 @@ message StartBarcodingRequest {
string output_reads_directory = 2;

// Enable gzip compression of output FASTQ files.
//
// DEPRECATED: This option does not have any effect - the offline barcoding no longer has the ability to compress fastq output.
bool compress_fastq = 4;

// Recursively find fast5 files to basecall in the `input_reads_directories`.
Expand All @@ -246,6 +249,13 @@ message StartBarcodingRequest {
// Options to control barcoding performed once basecalling reads is complete.
analysis_configuration.BarcodingConfiguration barcoding_configuration = 10;

enum OutputFormat {
BAM = 0;
FASTQ = 1;
}

// The type of file format to use for the output, default is BAM.
OutputFormat output_format = 12;
}

message StartBarcodingResponse {
Expand Down Expand Up @@ -313,6 +323,9 @@ message StartRequest {
basecaller.StartBarcodingRequest start_barcoding_request = 3;
basecaller.StartAlignmentRequest start_alignment_request = 4;
basecaller.StartPostProcessingProtocolRequest start_post_processing_protocol_request = 5;

// Since 5.8
analysis_workflows.ProxyRequest proxy_request = 6;
}
}

Expand Down
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